Busch was making his final stop for four tires and fuel on Lap 65 when the caution flag waved for debris on the track.
With all the other lead-lap cars making their final stop, Busch went back to the top of the leader board.
In the inaugural Indiana 250, Busch led 51 of the first 65 laps before getting shuffled back in the field as a result of pit strategy, crashed and finished 22nd.
He led 92 of 100 laps Saturday.
It turned out to be a bad day at IMS for Sam Hornish Jr., who entered the day as the points leader. Hornish was unable to finish the race when on Lap 64 his Ford overheated.
On the restart, Busch pulled away from Logano, who used a two-tire pit stop on Lap 64 to gain track position.