One shot behind, McIlroy took the lead with a three-shot swing on No. 7 and never let Koepka or Xander Schauffele catch him in the Tour Championship.
McIlroy closed with a 4-under 66, a score that would have won the Tour Championship in any scoring format. He finished four shots ahead of Schauffele.
He joined Tiger Woods as the only players to win the FedEx Cup twice since it began in 2007.
And this time, McIlroy had the stage to himself. A year ago, he was merely a bystander playing in the final group as Woods capped off his comeback by winning at East Lake.
This time, the chants were for him.