McIlroy secured the FedEx Cup for a third time in his career with an excellent final round 66 to take victory by a single stroke from Scheffler and Sungjae Im.
The players had begun the week at East Lake on staggered scores determined by their place in the FedEx Cup standings, and Scheffler re-opened his lead to six shots after the conclusion of the weather-delayed third round on Sunday morning.
But his Northern Irish playing partner was able to capitalise on an error-prone round of 73 from the 26-year-old.
After leaving the 18th green, McIlroy was congratulated by the parents of the Masters champion, telling them that he felt their son deserved to take victory after an “unbelievable year” that included three other PGA Tour wins to go along with that maiden major triumph at Augusta.
“I’m sorry,” McIlroy said to Scott and Diane Scheffler. “He deserves it.
“He’s had an unbelievable year.”
Scheffler’s father repied: “So did you. Good playing.”
“Congrats,” added Diane. “Good job. Great job.”
The Northern Irishman earned $18m (£15.36m) in prize money with victory at the East Lake course, bouncing back from the disappointment of fading to finish third at The Open in July.
“What a week, what a day,” McIlroy told Sky Sports.
“I feel like Scottie deserves at least half of this. He’s a hell of a competitor. It was an honour to battle with him.
“St Andrews was really hard for me. It was a tough one to get over.
“This softens the blow a little bit. It doesn’t make it that much easier to get over, but it’s great to end the season on a high note like this.”
McIlroy also hoped the pair’s duel served as a reminder of the PGA Tour’s value among yet more rumours of high-profile defections to the Saudi-backed LIV Golf Series.
The 33-year-old has been a prominent critic of the breakaway events, with Open champion Cameron Smith widely expected to be among the next group of players to join.
“I believe in the game of golf, I believe in this Tour in particular, I believe in the players on this Tour,” McIlroy explained.
“It’s the greatest place in the world to play golf, bar none, and I’ve played all over the world.
“This is an incredibly proud moment for me, but it should also be an incredibly proud moment for the PGA Tour. They have had some hard times this year but we are getting through it and that was a spectacle out there today.
“Two of the best players in the world going head-to-head for the biggest prize on the PGA Tour and I hope everyone at home enjoyed that.”