The AFC West leaders took a 10-3 lead in the first quarter, but their divisional rivals hit back to end a four-game losing streak.
The Broncos quarterback told reporters: "I give San Diego's defense a lot of credit. They played well on defense and we were not as sharp, we just didn't play as well and didn't stay on the field.
"We didn't have the ball much and when we had it though, we didn't do enough with it. Give San Diego credit, they played better than we did.
"I thought we had pretty good practices on a short week. I thought we prepared to play a division game on the short week and thought we were prepared to play. We certainly just didn't play as well as we would have liked."
The Broncos are yet to clinch their division, but are already guaranteed at least a wild card spot in this season's playoffs.