McIlroy was three shots behind with three holes to play Sunday in the Tour Championship.
Dustin Johnson surprisingly was never a factor and he hit too many errant shots on the front nine and never recovered, closing with a 73.
He looked to put the perfect finish onto his big day when he hit over the water to 6 feet for an eagle putt on the par-5 18th in the first playoff hole.
McIlroy was ready to pump his fist until his eagle putt slid by, and he removed his cap in disbelief.
He twice was runner-up to Jason Day, and once to McIlroy.