Larson thrived out of a late restart with smart moves and a clever lane choice on Fontana's five-wide asphalt. The native Californian won the Xfinity race at Fontana for the second time in his Chip Ganassi Racing Chevrolet.
Larson, the Cup series points leader, is also on the pole for Sunday's race with a chance for a weekend sweep.
Kyle Busch was third, with Erik Jones in fourth and rookie William Byron in fifth.
Cup regulars Larson, Busch and Logano dominated the Xfinity race on a cloudy day at Fontana. Logano twice rallied from far back in the pack to challenge the leaders.