Logano, who started from pole, overcame a stop-and-go penalty early in the caution-filled race and kept Keselowski at bay after a restart with four laps to go in the 82-lap race. It's the first road course win of his career and 25th in NASCAR's second-tier series.
The Penske duo led all but three laps in a race on the 2.45-mile layout that was delayed by seven cautions for 20 laps.
Series points leader Chris Buescher was third, followed by
Chase Elliott, second in points, was seventh.
AJ Allmendinger has won the Sprint Cup pole at Watkins Glen International.
Allmendinger also won the pole on the road course at Sonoma in June. He turned a fast lap of 127.839 mph to edge
Five-time Watkins Glen winner
Road America returns to IndyCar schedule
IndyCar officials announced next year's schedule will include a race at Road America in Elkhart Lake, Wisconsin.
Practice and qualifying on the 14-turn, 4.048-mile road course will be held June 24-25. The race is set for June 26.
Twenty-five races were held at Road America from 1982-2007, some with the now defunct Champ Car Series -- IndyCar's rival during the open-wheel split.
The schedule released Saturday shows next year's race will be the first since the two series merged in 2008.
Derrick Walker, IndyCar's outgoing president of competition, called the venue, built in 1955, a "classic road course" with challenging corners that takes advantage of the natural terrain.