The Vikings took a 10-9 lead with 1:54 to play on a 1-yard pass from Sage Rosenfels to Matt Asiata, the game's only touchdown.
San Diego then marched 53 yards in nine plays and Novak produced his second field goal of the night.
Nate Kaeding kicked field goals of 50 yards in the first period and 54 yards in the fourth for the Chargers.
The Chargers improved to 3-0 in the exhibition season and Minnesota is 1-2.
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