Harvick fell just short of a three-race West Coast sweep, but finished second to extend his remarkable streak of top-two Sprint Cup finishes to eight races dating to last season.
Keselowski led only one lap, but capitalized on two late restarts to a green-white-checkered finish.
After getting four tires on the first late caution, Keselowski then slipped underneath Busch for the decisive pass, taking full advantage of the California speedway's wide track for his first career win at Fontana in his Team Penske Ford.
Busch finished third in his second race back from a suspension.
