The Broncos (11-3) have already clinched a place in the postseason but have now given Kansas City (10-3) a chance to snatch the division title from their grasp.
The Chargers (7-7) trail Baltimore (7-6) and Miami (7-6) in the chase for the last wildcard spot.
"This win says a lot about the coaches and the players, how hard they've worked to get to this point," Chargers rookie head coach and former Broncos offensive coordinator Mike McCoy said.
"We knew we had a tough game coming here but everyone stepped up, we ran the football extremely well and it was a great team effort.
"The defense did a great job overall, I'm very proud of them."
After falling behind early the Chargers scored 21 unanswered points, including two touchdown receptions from rookie wide receiver Keenan Allen in the second quarter, then squashed Manning's attempted comeback with a clutch interception late in the game.
With Denver down 24-17 and more than five minutes left, Thomas Keiser pulled in the crucial pick for the Chargers after Corey Liuget pressured Manning and knocked his arm during the throw.
It allowed Nick Novak to kick a 35-yarder and pad the lead to 10 points. Denver scored a late field goal but had no time to push to tie the game.
Chargers quarterback Phillip Rivers was 12 of 20 for 166 yards and two touchdowns, while Manning finished 27 from 41 night for 289 yards, two touchdowns and an interception.
Ryan Mathews rushed for 127 yards and a touchdown for San Diego.
The Broncos opened in clinical fashion, using only seven plays and just over three minutes on the opening drive before Manning connected with Andre Caldwell from 15 yards for a touchdown.
The Chargers could only respond with a 38-yard field goal from Novak but those three points were negated soon after when Matt Prater kicked one through from 32 yards to leave it 10-3 to Denver after a quarter.
But the second quarter was all San Diego with Rivers sending rookie Allen in for two touchdowns, the first featuring a great hurdle into the endzone and the second a clever catch while falling.
The 17-10 halftime lead was extended to 24-10 soon after the main break when Matthews rushed over from 23 yards on the opening drive.
Manning tried to bring his team back and found Caldwell for his second score early in the final quarter but the interception proved costly and San Diego took the win.