Ryan Matthews contributed 127 rushing yards and a score for the Chargers, who kept their playoff chances alive by advancing to 7-7.
Denver, having already clinched no worse than a wild card berth, had a chance to capture the AFC West title this weekend but the Broncos generated their fewest number of points all season while dropping to 11-3.
Kansas City can move into a tie for the division lead with the Broncos by defeating Oakland Sunday, although Denver holds the tiebreak edge over the Chiefs having won both their meetings this season.
Rivers threw scoring throws of 19 and 10 yards to Allen on consecutive possessions in the second period to give San Diego a 17-10 lead at halftime.
The Chargers then drove 80 yards in eight plays the first time they had the ball in the second half with Matthews scoring on a 23-yard run.
Peyton Manning's second touchdown pass of the game, a 5-yarder to Andre Caldwell, brought the Broncos within seven early in the fourth quarter. San Diego boosted its lead to 10 points on a Nick Novak field goal with 2:36 remaining.
Manning's two touchdown throws left him three away from tying the single-season record of 50 set by New England's Tom Brady six years ago.
Manning completed 27-of-41 throws for 289 yards. Rivers went 13-of-20 for 166 yards.