The home team led after the first quarter, but were stung by two touchdown passes from Philip Rivers in the second, before eventually triumphing 27-20 at Sports Authority Field.
It leaves John Fox's men 11-3 for their season.
Rivers found Keenan Allen twice to see the visitors take a 17-10 lead into half time, and they went further ahead after the break when Ryan Mathews took a hand-off from the quarterback and darted into the endzone.
The Broncos tried to mount a comeback in the fourth quarter, with Manning once again finding Caldwell for a four-yard score.
However, a 35-yard kick from Novak stretched the Chargers' lead to 10, and the only reply that the Broncos could muster was another kick from Prater.