"It's pretty awesome to be able to win here," Busch said of the legendary Indy track, where Busch won the Indiana 250 in his No. 54 Toyota.
It was Busch's eighth Nationwide Series victory this season and his first at Indianapolis.
He dominated most of Saturday's race, leading 92 of its 100 laps, but Busch nearly saw victory slip away after the final restart with six laps remaining.
Scott, a Chevrolet driver still searching for his first Nationwide win, moved past Busch for the lead. But Busch soon reclaimed the front spot and held it until the checkered flag.
Scott finished second and Logano -- who like Busch mainly races in NASCAR's top-level Sprint Cup Series -- finished third.
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