Johnson had gone by Busch with 17 laps remaining. But on the restart after the ninth caution period, Busch went high on the track at Chicagoland Speedway and got by Johnson and held on for yet another victory.
Johnson, driving the No. 48 Chevrolet for Hendrick Motosports, is the two-time defending Sprint Car Series champion.
Busch has 14 victories this season, spanning NASCAR's three series. He won a Nationwide Series race on the same track Friday night.