The Hoosiers (26-5, 14-4 Big Ten) used a 6-0 run down the stretch, capped by Zeller's basket, to rally for the victory and their first outright conference crown since 1993.
They only secured the victory when Jordan Morgan's put-back try off Trey Burke's missed lay-up rimmed out just before the final buzzer.
Zeller ended with 25 points and 10 rebounds while Victor Oladipo provided 14 and 13 for Indiana, which won six of its final eight games to wrap up the conference title an earn a No. 1 seed in the upcoming Big Ten Conference Tournament.
Burke netted 20 points for the Wolverines (25-6, 12-6), who fell at home for the first time this season.
Michigan earned a fifth seed in the upcoming conference tourney.