Reche Caldwell caught his second pass of the season and first touchdown, a 28-yard grab to give San Diego a 31-17 lead heading into the fourth quarter.
The Chargers extended their lead to 17 points with a Nate Kaeding field goal from 21 yards out.
Bhawoh Jue intercepted a Tom Brady pass with just over four minutes to go in the game. Brady would not return to the game. Donnie Edwards intercepted a Matt Cassel pass batted by Shaun Phillips and pitched it to Clinton Hart who ran it back for a touchdown and 41-17 win.
After Adam Vinatieri missed a field goal wide right on the Patriots opening drive of the game, San Diego placekicker Nate Kaeding drilled his attempt from 42 yards out to give the Chargers a 3-0 lead. Vinatieri would convert on a 24-yard field goal to tie the game right before the half.
The Patriots answered quickly with Tom Brady going 4-for-6 for 58 yards before Corey Dillon punched it in from a yard out.
The Chargers overcame two offensive holding calls and a false start on their first touchdown drive of the game. Drew Brees went 6-for-6 for 71 yards on the drive capping it off with a touchdown pass to Keenan McCardell from 11 yards out.
Bethel Johnson came back with a huge 57-yard return on the ensuing kickoff. Shaun Phillips knocked the ball out with four Chargers defenders in the area but the Patriots recovered the loose ball. It took the Patriots just 52 seconds to regain the lead when Brady hit Tim Dwight for a 30-yard touchdown reception.
A 44-yard pass interference call on a ball thrown to Eric Parker with Eugene Wilson in coverage gave the Chargers the ball at the eight-yard line. Two plays later, Tomlinson willed the ball through the Patriots' defense to extend his record of consecutive games with a rushing touchdown to 16.