Williams started the 2009 season averaging 55 yards per game in the first four games. He found the endzone twice in that stretch. In Week 6, he had 30 carries for 152 rushing yards and two rushing touchdowns in a 28–21 victory over the Tampa Bay Buccaneers. In Week 7, Williams recorded a 77-yard run against the Arizona Cardinals for the longest rushing play in franchise history, breaking his own mark set in 2007. Williams would hold this mark until Christian McCaffrey recorded an 84-yard run in 2019. In the game, Williams totaled 23 carries for 158 rushing yards in the 34–21 victory. He followed that up with 21 carries for 149 rushing yards and two rushing touchdowns in a 30–20 loss to the New Orleans Saints. Despite missing all of three games and most of two more due to injury, Williams managed to rush for 1,117 yards and seven rushing touchdowns on 216 carries, as well as receiving for 252 yards on 29 catches, earning himself a spot in the Pro Bowl. He and Jonathan Stewart became the first running back duo since the 1970 merger to rush for 1,110 yards apiece (with Stewart rushing for 1,133 yards), as well as becoming the first running back in franchise history to rush for 1,000 in consecutive seasons.