2012 San Francisco 49ers season The San Francisco 49ers season was the franchise ' s 63rd season in the National Football League , the 67th overall , the second under the head coach / general manager tandem of Jim Harbaugh and Trent Baalke . After going 13 - 3 and reaching the NFC Championship the year before , the 49ers topped that success with their first NFC championship since 1994 as well as their sixth overall as a franchise , overcoming a 17 - 0 deficit to defeat the Atlanta Falcons 28 - 24 on January 20 , 2013 in the NFC title game . However , the season ended with their first ever defeat in the Super Bowl , falling to the Baltimore Ravens , 31 – 34 . Quarterback controversy . Quarterback Alex Smith missed two starts mid - season after suffering a concussion , and backup Colin Kaepernick successfully filled in . A quarterback controversy began . Smith was ranked third in the NFL in passer rating ( 104 . 1 ) , led the league in completion percentage ( 70 % ) , and had been 19 – 5 – 1 as a starter under Harbaugh , while Kaepernick was considered more dynamic with his scrambling ability and arm strength . After Smith was fully recovered , Harbaugh chose Kaepernick as the starter for the 8 – 2 – 1 49ers , but also stated that the assignment was week - to - week and not necessarily permanent . However , Kaepernick started the remainder of the season through the Super Bowl . Schedule . Preseason . The 49ers ' preseason schedule was announced on April 17 , 2012 . Game summaries . Regular season . Week 1 : at Green Bay Packers . With the win , the 49ers started their season 1 - 0 . Week 2 : vs . Detroit Lions . With the win , the 49ers improved to 2 - 0 . Week 3 : at Minnesota Vikings . With the loss , the 49ers fell to 2 - 1 and into a tie with the Seahawks in 2nd place in the NFC West behind the 3 - 0 Cardinals . Week 4 : at New York Jets . After a tough road loss , the Niners continued on the road to face the Jets . The team would improve to 3 - 1 as they handed the Jets their 2nd shutout home loss in 2 years . Week 5 : vs . Buffalo Bills . With the huge win , the 49ers improved to 4 - 1 . 2 - 0 against the AFC East . Week 6 : vs . New York Giants . With the huge loss , the 49ers fell to 4 - 2 . Week 7 : vs . Seattle Seahawks . With the win , the 49ers improved to 5 - 2 . Week 8 : at Arizona Cardinals . Alex Smith completed 18 - of - 19 passes for 232 yards and three touchdowns without an interception in a 24 – 3 Monday night win over Arizona . With the win , the 49ers went into their bye week at 6 - 2 . Week 10 : vs . St . Louis Rams . Smith suffered a concussion in the second quarter , throwing a touchdown with blurred vision before exiting the game . He was replaced by Colin Kaepernick , and the game ended in a 24 – 24 tie . With the tie game , the Niners ' season stood at 6 - 2 - 1 . This would also be the first NFL tie game since 2008 when the Bengals and Eagles played to a 13 - point tie . This is also the first tie game between both the Rams and Niners since a 20 - 20 tie game in 1968 . Week 11 : vs . Chicago Bears . Kaepernick started his first NFL game with Smith out with a concussion from the previous week . Kaepernick completed 16 of 23 for 246 yards with two touchdowns and no interceptions in a 32 - 7 win against a strong Bears defense . 49ers head coach Jim Harbaugh spoke highly of Kaepernick ' s performance after the game , leaving open the possibility of Kaepernick continuing to start . " Usually tend to go with the guy who ' s got the hot hand , and we ' ve got two quarterbacks that have got a hot hand , " Harbaugh said . He dismissed any rule that a player should not lose their starting job due to an injury . With the win , the 49ers improved to 7 - 2 - 1 . Week 12 : at New Orleans Saints . Smith was cleared to play the day before the game , but Harbaugh chose not to rush him back and again started Kaepernick . In a rematch of the 2012 playoffs against New Orleans , the 49ers won 31 – 21 with Kaepernick throwing for a touchdown and running for another . The 49ers defense also returned two Drew Brees interceptions for touchdowns . With the win , the Niners improved to 8 - 2 - 1 and also to 2 - 0 under Kaepernick as a starter . Week 13 : at St . Louis Rams . With their loss to the Rams , the 49ers fell to 8 - 3 - 1 on the season . Kaepernick ' s record as a starter dropped to 2 - 1 . Week 14 : vs . Miami Dolphins . With the win the 49ers improved to 9 - 3 - 1 giving them their 2nd straight winning season and moving to 3 - 0 against the AFC East . Also Kaepernick ' s starting record improved to 3 - 1 . Week 15 : at New England Patriots . With the win the 49ers improved to 10 - 3 - 1 and became the only team in the NFC West to defeat all 4 AFC East teams . Kaepernick ' s starting record also improved to 4 - 1 . Week 17 : vs . Arizona Cardinals . The Niners returned home for a Week 17 rematch against the Cardinals . Needing a win to capture the NFC West crown , the team would be down 3 - 0 after the first quarter . But rallied from a 7 - 6 halftime lead to win the game 27 - 13 and finished the season with their 2nd straight division title and of course the NFC ' s # 2 seed with a record of 11 - 4 - 1 while going 5 - 2 under Kaepernick as a starter . Postseason . NFC Divisional Playoffs : vs . # 3 Green Bay Packers . In his first career playoff game , 25 - year old 49ers quarterback Colin Kaepernick rushed for 181 yards and two touchdowns , setting both the NFL single - game record for rushing yards by a quarterback as well as the 49ers postseason record for rushing , regardless of position . He also passed for 263 yards and two scores . Overall , San Francisco racked up 579 yards , including a franchise record 323 rushing yards , and scored a touchdown in every quarter to earn their second consecutive trip to the NFC championship game . However , Kaepernick didn ' t get off to a good start . Less than two minutes into the game , he threw a pass that was intercepted by Sam Shields and returned 52 yards for a touchdown . But he quickly rallied his team back , completing a 45 - yard pass to running back Frank Gore before taking the ball into the end zone himself on a 20 - yard run . Later in the period , Green Bay took a 14 – 7 lead with Aaron Rodgers ' 44 - yard completion to James Jones setting up an 18 - yard touchdown run by DuJuan Harris . The Packers then forced a punt , but returner Jeremy Ross muffed the kick and C . J . Spillman recovered it for San Francisco on the Packers 9 - yard line . Two plays later , Kaepernick tied the score at 14 with a 12 - yard touchdown pass to Michael Crabtree . Then defensive back Tarell Brown intercepted a pass from Rodgers , setting up Kaepernick ' s second touchdown pass to Crabtree , this one from 20 yards out . With 2 : 39 left in the half , Rodgers ' 20 - yard touchdown pass to Jones tied the score at 21 . But on the 49ers next drive , a pair of runs by Kaepernick for gains of 19 and 17 yards enabled David Akers to kick a 36 - yard field goal , sending the teams into their lockers rooms with San Francisco leading 24 – 21 . In the third quarter , Green Bay drove 76 yards in 9 plays , featuring a 30 - yard reception by Greg Jennings and scored a Mason Crosby field goal . But the tie turned out to be short lived . On the third play of their next drive , Kaepernick faked a handoff , rolled right , and took off for a career long 56 - yard touchdown run , retaking the lead at 31 – 24 . Then after a punt , he completed a 44 - yard pass to tight end Vernon Davis , setting up Gore ' s 2 - yard touchdown run on the first play of the fourth quarter . Following another punt , Kaepernick led the 49ers back for more points , this time on a 93 - yard drive . First he ran for a 16 - yard gain , and later he completed a 17 - yard throw to tight end Delanie Walker . On the next play , Gore ' s 26 - yard burst moved the ball to the Packers 27 - yard line . Anthony Dixon eventually finished the 11 - play drive with a 2 - yard touchdown run , making the score 45 – 24 . With under a minute left , Rodgers threw a 3 - yard touchdown pass to Jennings . But any hope of a miracle comeback was dashed when Walker recovered the ensuing onside kick attempt . Crabtree was the top receiver of the game , with 9 catches for 119 yards and two touchdowns . Gore rushed for 119 yards and a touchdown , while also catching two passes for 48 yards . Linebacker Patrick Willis had 7 tackles and a sack . Rodgers finished 26 / 39 for 257 yards and two touchdowns , with 1 interception , while also rushing for 28 yards . Kaepernick finished the game responsible for more yards gained ( 444 ) then the entire Packers team ( 352 ) NFC Championship : at # 1 Atlanta Falcons . San Francisco overcame a 17 - point deficit , the largest comeback ever in an NFC championship game , to earn their sixth Super Bowl appearance in franchise history . Atlanta dominated the first quarter , mainly on plays by receiver Julio Jones , who caught 5 passes in it for 100 yards , including a 46 - yard touchdown catch on their opening drive , and a 27 - yard reception on their next drive to set up a Matt Bryant field goal . Following a punt , Matt Ryan hit Roddy White for a 23 - yard gain on the last play of the first quarter . Then he threw a 20 - yard touchdown pass to Jones on the first play of the second , giving the Falcons a 17 – 0 lead . This time San Francisco struck back with an 80 - yard scoring drive , with Frank Gore rushing for 20 yards and Vernon Davis catching a pass for 27 . LaMichael James finished the drive with a 15 - yard touchdown run . Then after forcing a three - and - out , Colin Kaepernick rushed for 23 yards and completed three passes to Davis for 48 yards , the last a 4 - yard touchdown pass to make the score 17 – 14 . But Atlanta stormed back as Ryan completed five passes for double - digit gains on their next drive , the last one a 10 - yard score to tight end Tony Gonzalez with 25 seconds left in the half . The 49ers took the opening kickoff and drove 82 yards , with Kaepernick completing two passes to Randy Moss for 38 yards and one to tight end Delanie Walker for 20 . Gore completed the drive with a 5 - yard touchdown run , cutting their deficit to 24 – 21 . On Atlanta ' s ensuing possession , defensive back Chris Culliver gave San Francisco a great chance to tie or take the lead by intercepting a pass from Ryan and returning it to the Falcons 25 - yard line . But San Francisco failed to gain a first down and came up empty when David Akers hit the uprights on a 38 - yard field goal try . Later on , the 49ers got another scoring opportunity when defensive lineman Aldon Smith recovered a fumble from Ryan on his own 40 - yard line . They subsequently drove deep into Falcons territory , but once again they failed to score when defensive back Dunta Robinson stripped the ball from Michael Crabtree on the 1 - yard line as he trying to get in for the go - ahead score , and linebacker Stephen Nichols recovered it . With 12 minutes left in regulation , Ted Ginn , Jr . ' s 20 - yard punt return gave San Francisco the ball on the Falcons 38 - yard line . Five plays later , Gore scored his second touchdown on a 9 - yard run , giving the 49ers their first lead of the game at 28 – 24 . Atlanta responded with a drive to the 49ers 13 - yard line , but consecutive incompletions on third and fourth down caused a turnover on downs with just 1 : 13 left in the game . Atlanta managed to force a punt and get the ball with 13 seconds to go . Ryan completed a pass to Jones on the final play , but he was tackled at the 49ers 35 - yard line as time expired . Kaepernick finished 16 / 21 for 233 yards and a touchdown , along with 21 rushing yards . Davis caught 5 passes for 106 yards and a score . Gore rushed for 90 yards and two touchdowns . Ryan completed 30 of 42 passes for 396 yards and three touchdowns , with one interception . Jones caught 11 passes for 182 yards and two touchdowns , while White had 7 receptions for 100 yards . Gonzalez caught 8 passes for 78 yards and a score . Super Bowl XLVII : vs . Baltimore Ravens . For what seemed like a blowout win for the Ravens , the Niners would rally in the 2nd half outscoring the Ravens 25 - 13 but fell 3 points short of a victory as the Ravens won it 34 - 31 after an on - purpose safety . This marks the first time ever in franchise history the Niners have lost a super Bowl as their overall record dropped to 13 - 5 - 1 on the season and 2 - 1 in postseason . As well as making them 5 - 1 in Super Bowls .