It appeared Maddon had already been tossed before coming onto the field to complain to plate umpire D.J. Reyburn during an at-bat by Starlin Castro to start the sixth. Castro ended up flying out to right in a game the Cubs led 5-2.
Chicago entered with a season-worst four-game losing streak.
Maddon has been ejected twice this year. The other came April 17 against San Diego.