San Diego went further ahead early in the second when Novak added three more points with a 36-yard field goal to make the score 10-0.
Allen helped to extend San Diego's lead having teamed up with Rivers again, this time to produce a four-yard pass, pushing the scores to 17-0.
Rivers was then in the mix of things again as he delivered a neat six-yard pass to Danny Woodhead at the end of the quarter to leave the Chargers 24-0 up at half time.
The Giants immediately began to erode the Chargers' advantage, with Peyton Hillis grabbing an early touchdown in the third.
Nevertheless, Mike McCoy's team wrapped up victory with two field goals from Nick Novak in the fourth.