Stewart held off Marcos Ambrose in the closing laps to become the road course king at the 2.45-mile track.
"This is my house right here," Stewart said after taking his first road course event as a driver and owner in the Sprint Cup Series. "We've run really well here the last eight years."
Stewart has finished either first or second in the last six races at Watkins Glen. It was his third victory this season and the 36th of his Sprint Cup career.
Thundershowers at Watkins Glen Sunday forced NASCAR officials to postpone the 90-lap race one day.
Ambrose finished second, his career-best in the series. Ambrose won the Nationwide event Saturday at Watkins Glen.
Carl Edwards came in third. Kyle Busch, last year's winner at Watkins Glen, was fourth.
Copyright 2009 by United Press International.