The Hoosiers (1-0) have now won 14 consecutive season-openers and 27 straight home-openers.
The Seawolves (0-1) were led by Anthony Jackson with 14 points and hung in the game early.
After giving up an 18-14 lead, an ugly sequence turned the game. Stony Brook's Al Rapier drew one foul and the Seawolves' Danny Carter was ejected when a replay review showed he had intentionally punched Zeller in the midsection during the same possession. Indiana made three free throws on four attempts, starting an 18-4 run that made it 40-25.
Stony Brook never got back within double digits.