Ryan Mathews ran for 127 yards and a touchdown and San Diego quarterback Philip Rivers threw two touchdown passes to Keenan Allen in the AFC West division clash.
Rivers was 12-of-20 for 166 yards for the Chargers, who improved to 7-7 and moved a half-game behind the Baltimore Ravens and Miami Dolphins for the AFC's second wild-card playoff berth.
Manning completed 27-of-41 passes for 289 yards with two touchdowns and an interception for the Broncos, who fell to 11-3.
Already assured of at least a wild-card berth, the Broncos are still battling the 10-3 Kansas City Chiefs for the AFC West crown.
Denver have the upper hand over the Chiefs, owning the head-to-head tiebreaker thanks to two wins over Kansas City this season.
Even if they win their divsion, however, the Broncos could lose out in the race to capture the top seed in the American Conference. The 10-3 New England Patriots are now very much in the running for the top spot as they visit Miami on Sunday in an AFC East division clash.
"You can analyse it any way you want ... I thought we prepared to play a division game on the short week, and thought we prepared to play, we didn't play as well as we would have liked," Manning said.
"It's hard to pinpoint a reason right now.
"There were some mistakes made out there in all three phases that were critical, and we weren't able to overcome them."
Denver's defeat was a boon for the Patriots, but the Dolphins have plenty to play for on Sunday as well.
Tied with reigning Super Bowl champions Baltimore for the sixth and final AFC playoff spot, Miami need every win they can get over the last three weeks of the regular season.
Elsewhere on Sunday, the Chicago Bears will have quarterback Jay Cutler back from injury against Cleveland.
Other games on Sunday see Washington at Atlanta, San Francisco at Tampa Bay, Seattle at the New York Giants, Houston at Indianapolis, Buffalo at Jacksonville, Philadelphia at Minnesota, the New York Jets at Carolina, Green Bay at Dallas, New Orleans at St. Louis, Arizona at Tennessee and Cincinnati at Pittsburgh.