Schottenheimer said Brees will undergo tests on his labrum and might need surgery.
Brees dropped back to pass from his end zone late in the second quarter and was blindsided on a blitz by safety John Lynch. Brees fumbled and was hit again while going for the ball, which was recovered by Denver's Sam Brandon at the 1-yard line. Tatum Bell scored on the next play to give the Broncos a 14-0 lead.
Brees was examined on the sideline, then was taken to the locker room. He was replaced by Philip Rivers, who finished the game for the Chargers.
Brees left immediately after the game and did not talk to reporters.
Although the Chargers already had been eliminated from the playoffs, coach Marty Schottenheimer didn't plan to use Rivers, a second-year pro, unless Brees got hurt.
Rivers had been in for one play this season, taking a knee to end a 48-10 win over Buffalo on Nov. 20.