2009 San Francisco 49ers season The 2009 San Francisco 49ers season was the franchise ' s 64th season , and the first full year with Mike Singletary as head coach after being named interim head coach in 2008 . It is the seventh year in which the 49ers have their seventh offensive coordinator . They were looking to improve upon their 7 – 9 record from 2008 with the 10th overall pick in the 2009 NFL Draft , The 49ers started the 2009 season hot by winning three of the first four games . Their only loss in that span was against the Minnesota Vikings on a last - second , 32 - yard touchdown from QB Brett Favre to WR Greg Lewis . With that , and a week - 5 blowout loss against the Atlanta Falcons , the team got a bad omen for the remainder of the year . The 49ers ' defense , led by linebacker Patrick Willis , kept the 49ers in games , while their offense was inconsistent . Most of the blame was due to their weak offensive line , namely , the injury of left tackle Joe Staley in a week 7 game against the Indianapolis Colts . The 49ers won a week 12 home game over the Jacksonville Jaguars , 20 – 3 . The win helped keep the 49ers ' season alive . Going into week 13 against the Seattle Seahawks , the 49ers were heavily favored to win the game ; however , critical mistakes in the game cost them the win and gave the team a huge blow of any chances of making the playoffs . The following week on Monday Night Football , the 49ers played the Arizona Cardinals , who were trying to clinch the NFC West . The 49ers ' defense came out and exploded on the Cardinals top - ranked offense , causing them to turn over the ball 7 times . This was the first time San Francisco caused 7 or more turnovers in a game since forcing eight against the New Orleans Saints on September 14 , 1997 . The 49ers won the game 24 – 9 , keeping their very slim playoff hopes alive . The next week they were defeated by the Philadelphia Eagles . The loss officially wiped out the 49ers from playoff contention . Despite being benched for 5 and a half games , Alex Smith came in and threw for a career - best 2 , 350 yards , 18 touchdowns , and 12 interceptions . Frank Gore rushed for 1 , 120 yards and 13 touchdowns . He was awarded his second Pro Bowl appearance . Tight end Vernon Davis turned his career around by leading the team with 965 yards and 13 touchdowns – which tied the single - season record for most touchdowns by a tight end . Rookie wide receiver Michael Crabtree , who held out the first four games of the season , was able to put up solid numbers , with 625 receiving yards , 48 receptions , and 2 touchdowns . On defense , Patrick Willis , for the second time in his first three seasons in the league , led the NFL with 152 tackles and helped the 49ers become one of the best defensive units in the NFL . He was awarded his third straight Pro Bowl appearance . Offseason . Coaching changes . The 49ers released Mike Martz on December 30 , 2008 . One day following the firing of Martz , the 49ers released quarterbacks coach Ted Tollner and running backs coach Tony Nathan . " To get where we needed to go , I felt those decisions needed to be made at this time , " said Mike Singletary . Tony Nathan ' s replacement came on January 7 , 2009 when former 49ers ' fullback Tom Rathman agreed to become the new running backs coach . Before the 49ers found a new quarterbacks coach , they introduced two new coaching positions on January 12 , 2009 . Mike Singletary ' s nephew Vantz Singletary became the 49ers ' inside linebackers coach , while Al Harris was signed as the 49ers ' pass rush specialist coach . One month after the firing of Martz , Jimmy Raye was finally hired as offensive coordinator , making him the seventh offensive coordinator in seven years for the 49ers . Along with the hiring of Raye , Ted Tollner ' s replacement Mike Johnson was signed as the 49ers ' quarterback coach . The 49ers ' next coaching addition would be Jason Michael as an offensive assistant on March 6 , 2009 . Offensive coordinator search . Two days after Mike Singletary was hired as San Francisco ' s head coach , Singletary fired offensive coordinator Mike Martz . " I am not what he is looking for offensively . I understand that , " said Martz in a statement released by the club . With the firing of Martz , the 49ers guaranteed themselves their seventh offensive coordinator in seven years . Possible replacement candidates included Colts wide receivers coach Clyde Christensen , former Rams head coach Scott Linehan , Browns offensive coordinator Rob Chudzinski . After a second interview with the 49ers , Linehan was offered the position ; however , he declined the position stating that it was not right for his family . Soon after , Linehan accepted the offensive coordinator position for the Detroit Lions . Following , the 49ers interviews Broncos offensive coordinator Rick Dennison , former Boston College coach Jeff Jagodzinski , and Ravens quarterbacks coach Hue Jackson . In the same day as the interview with Jackson , the 49ers flew in former Atlanta Falcons head coach Dan Reeves for an interview for the position . Following the Reeves interview , the 49ers interviewed Hue Jackson a second time . One day after Jackson was interviewed , former New York Jets ' running back coach Jimmy Raye II was interviewed , making him the eighth offensive coordinator candidate to be interviewed by the 49ers . After interviewing with the 49ers , Raye was named the new offensive coordinator for the San Francisco 49ers ; coincidentally , Raye ’ s first NFL job was the wide receivers coach for the 49ers under Ken Meyer in 1977 . Raye stated that he and Mike Singletary shared a belief on how football should be played , that being a ground - based , physical football team . Raye has had successful years as a run - based offensive coordinator , namely with the 1984 Los Angeles Rams , when Eric Dickerson rushed for a league - record 2 , 105 yards . However , his recent success has been questionable . While being the Oakland Raiders ' offensive coordinator from 2004 to 2005 , the Raiders were 32nd and 29th in rushing offense , respectively . Nonetheless , while Raye was running backs coach for the New York Jets over the past two years , Jets ' running back Thomas Jones has finished each season with over 1 , 000 yards rushing . In the 2008 season , Jones finished the season with the 5th most rushing yards , behind only Adrian Peterson , Michael Turner , DeAngelo Williams , and Clinton Portis . Uniform change . In 1996 the 49ers changed their uniforms to a darker cardinal red , with the most recent change being updating their pants back to gold in 1998 . Eleven years later , the 49ers decided to once again modify their uniform . The uniform change rumors were confirmed by Andy Dolich at the 49ers ' State of the Franchise . When asked when they were going to change their uniforms " back to normal " , Dolich replied , stating , " Stay tuned . Don ’ t be surprised if you see championship colors back " . The uniforms were revealed on April 25 , 2009 during the first day of the draft . 49ers players Patrick Willis , Josh Morgan , Dashon Goldson , Joe Staley , and Moran Norris displayed the new jerseys and pants at the 49ers draft party . The new jerseys are very similar to the classic design , with minor changes to the sleeve stripes , the moving of secondary numerals to the top of the shoulders , and the inclusion of a " 49ers " ligature below the neck . The shade of red is also arguably slightly darker than the scarlet of classic jerseys , but significantly lighter than the cardinal red used in the 1996 – 2008 designs . Roster changes . Additions . The following are players signed by the 49ers in the 2009 off - season : † College football team ‡ Arena Football League team Departures . The following are players who were released by the 49ers in the 2009 off - season : Free agents . The following are players whose contracts expired at the end of the 2008 season : < nowiki > * < / nowiki > 2009 NFL Draft . After finishing the 2008 season with a 7 – 9 record , the 49ers held the 10th overall pick in the 2009 NFL Draft . Surprisingly , the Oakland Raiders opted to choose WR Darrius Heyward - Bey at the 7th pick instead of WR Michael Crabtree , who was considered the top wide receiver in the draft . Because of this , the 49ers were able to pick Crabtree at the 10th selection . " Once we got to 10 and Crabtree was there , it was over , " said general manager Scot McCloughan , " . . . this is great , this is outstanding . " Additionally , the 49ers traded their 2009 2nd - and 4th - round picks to the Carolina Panthers for their 2010 1st - round pick . Starting quarterback search . At the start of the 2008 season , JT O ' Sullivan was named the starting quarterback of the 49ers , beating out the injured Alex Smith and third - string Shaun Hill . However , after a performing poorly for the fist half of the season , O ' Sullivan was benched and Hill became the starting quarterback . By the season ' s end , Hill ' s numbers were solid ; however , even with a career passer rating of 91 . 6 going into 2009 , Mike Singletary has stated that Hill will not be named the starting quarterback for the 49ers . " There ’ s going to be competition for that spot , " said Singletary the 49ers ' State of the Franchise Meeting , " If Alex is back , there will be competition for that spot . " Just hours after Kurt Warner decided to sign with the Arizona Cardinals , the 49ers signed a one - year deal with quarterback Damon Huard . The signing of Huard brings veteran experience to the 49ers ' quarterback corp . On March 10 , Smith accepted a pay cut to stay with the 49ers . On top of the release of JT O ' Sullivan , last year ' s starting quarterback , to the Cincinnati Bengals , Hill , Smith , Huard , and draft pick Nate Davis will be competing for the starting quarterback position . Chasing Kurt Warner . Heading into the 2005 season , Arizona Cardinals ' quarterback Kurt Warner became a free agent . After being offered a two - year , $ 20 million contract by the Cardinals , Warner declined . Following , Warner decided to take a visit to the 49ers on March 2 , 2009 . The 49ers sent a private jet for Warner and his wife Brenda ; a limousine brought the couple to Silicon Valley , where the 49ers ' training complex is located . However , on March 4 , Warner resigned to the Cardinals for a two - year , $ 23 million deal . Many believe that the visit to California was a way to gain leverage on the Cardinals in order to raise the contract deal ; although Warner and his agent insists that was not the case . Restructuring Smith ' s contract . Alex Smith , the number one overall pick of the 2005 NFL Draft by the 49ers , was scheduled to make $ 9 . 625 million going into the 2009 season . However , with one - and - a - half seasons on the Injured reserve list , the 49ers asked Smith to renegotiate his contract . After returning from his honeymoon in the Maldives , Smith agreed to a pay cut at an undisclosed amount . With the cut , Smith says that he is ready to compete for the starting quarterback spot , primarily against Shaun Hill . " I ’ m glad it ’ s against Shaun , " Smith said , " He ’ s a great guy . I can ’ t think of a better guy to compete against . " Captains . On September 11 , 2009 , head coach Mike Singletary announced the 2009 season captains for the 49ers . They were center Eric Heitmann and tight end Vernon Davis for the offense ; linebacker Patrick Willis , linebacker Takeo Spikes and defensive end Justin Smith for the defense , and running back Michael Robinson for special teams . The captains were chosen by Singletary himself . Davis ' selection as captain represented a turnaround after he was benched during Singletary ' s first game as head coach in 2008 .