Harvick, a native of nearby Bakersfield, Calif., bypassed Johnson between turns three and four on the final lap and finished about two car lengths in front, claiming his first win at his home track in a Sprint Cup event.
Harvick's victory was his 15th in the series and handed team owner Richard Childress his first-ever Sprint Cup win at Fontana.
Kyle Busch led for 151 of the 200 laps but surrendered the lead to Johnson after touching the wall with two laps left, finishing third. His streak of three straight wins in NASCAR national touring events was snapped.
Matt Kenseth ended in fourth place and Ryan Newman garnered fifth Sunday.