His No. 48 Hendrick Motorsports Chevrolet crossed the finish line two seconds ahead of teammate Jeff Gordon.
The victory was the 150th for Hendrick Motorsports, Johnson's first of the season, and 24th of his Nextel Cup career.
"I knew once Jimmie got in front of me we weren't going to catch him," Gordon said.
Martin will remain the championship leader, six points ahead of Gordon (495-489).
Jeff Burton (453) is third and Johnson (406) jumped 11 places to fourth.
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