Andretti won the pole with a two-lap average speed of 170.515 mph around the mile oval. James Hinchcliffe was second at 170.418 for a 1-2 finish for the Andretti cars.
Will Power broke up an Andretti sweep by qualifying third at 170.212.
But Power was followed by defending race winner Ryan Hunter-Reay and E.J. Viso as the Andretti drivers proved they are the ones to beat Saturday in the 250-mile IndyCar race.
Sebastian Saavedra was sixth and Tony Kanaan was seventh as Chevrolet drivers swept the top seven spots.
Josef Newgarden was the highest qualifying Honda at eighth.
Andretti Autosport has won four of the past eight races at Milwaukee.
• Points leader Helio Castroneves insisted Friday that his race-winning car at Texas did not have a performance advantage from an illegal part that led to a failed post-race inspection.
IndyCar this week fined Penske Racing $35,000 and docked Roger Penske 15 owner points because the underwing height on Castroneves’ car was too low following Saturday night’s win. Penske Racing put the car in a wind tunnel Monday and determined it had no advantage from the part and actually raced at a disadvantage because Castroneves had three pounds less downforce and one pound more drag than if the wing was correct.
Castroneves, who said he was “very shocked” the car failed inspection, was thankful the team took that step.
ARCA SERIES: In Brooklyn, Mich,. Brennan Poole won the race at Michigan International Speedway, holding off pole-sitter Ryan Blaney by 0.567 seconds.
Poole led for only the last dozen laps of the 200-mile, 100-lap race in his No. 15 Toyota. Frank Kimmel finished third to remain a victory shy of matching Iggy Katona’s series record of 79 career wins.
Poole qualified second behind Blaney. The Texas driver has four career ARCA victories.