During the season, he was named a co-captain along with teammates Alex Smith, Walt Harris, Bryant Young and Keith Lewis.
It was announced the week after that he would rejoin the team as the starter at LT, but during the next game against the New York Giants he split time with his backup Adam Snyder.
Jennings sustained a high ankle sprain in the second quarter of the 49ers' loss to the Giants on October 21 and missed the subsequent two games.
On November 5 he was placed on Injured Reserve; coach Mike Nolan stated that Jennings was to undergo surgery to remove "loose bodies" in his ankle, effectively ending his 2007–2008 season.
Although he insisted on remaining on the sideline as an emergency backup, ultimately he was placed on injured reserve to undergo his 3rd shoulder surgery.