McIlroy shot four under for the day to finish 18 under for the Tournament, four shots better than Masters co-runner-up Xander Schauffele.
This is his second Tour Championship victory. He defeated Kevin Chappell and Ryan Moore in a playoff in 2016.
McIlroy earns $15 million with the result, which represents nearly a third of his career earnings prior to this Tournament.
The final round turned into a war of attrition, as only eight of the 30 golfers carded a score under par for the day. Schauffele was even par, while Brooks Koepka shot two over after entering the round atop the leaderboard with a one-shot lead over McIlroy.
Tour Championship Leaderboard—Top 10
1. Rory McIlroy (-18)
2. Xander Schauffele (-14)
T3. Justin Thomas (-13)
T3. Brooks Koepka (-13)
5. Paul Casey (-9)
6. Adam Scott (-8)
7. Tony Finau (-7)
8. Chez Reavie (-6)
T9. Patrick Reed (-5)
T9. Kevin Kisner (-5)
T9. Hideki Matsuyama (-5)
McIlroy appeared to be fading down the stretch following back-to-back bogeys on the 14th and 15th holes. He started the third round of the 2018 Tour Championship three shots back of Tiger Woods before carding a four-over 74 on the final day.
According to PGATour.com, his 69.80 fourth-round scoring average is 50th in the Tour, so he generally hasn't saved his best golf for Sundays this season.
The trend was seemingly continuing as McIlroy sent his drive on No. 16 into a bunker to the right of the fairway. The four-time major champion got onto the green in three shots and sank a nine-foot par putt to maintain a two-shot advantage on Schauffele.
That par save helped McIlroy lock back in mentally as he birdied No. 17 to build a three-shot gap between himself and Schauffele.
Buoyed by that comfortable breathing room, McIlroy crushed his drive on the 18th hole 337 yards. Not even a second-shot approach into the bunker slowed him down. He chipped out of the sand to within six feet of the cup, and his birdie putt was on the money to seal his third win of the season.
During his post-tournament interview, McIlroy referenced how he fell short in Atlanta in 2018:
"I didn't enjoy that walk last year like everyone else did. I played terribly, got myself into the final group, but I never took the fight to Tiger. Going up against the No. 1 player in the world today, he got one over on me in Memphis and I wanted to get some revenge today. To play like that alongside Brooks and get the win and win the FedEx Cup, it's awesome. It's amazing how different things can be in a year."
The Tour Championship brings a close to the 2019 PGA Tour season, so McIlroy will get a few months off before he's back to meaningful action.
Because of that, the momentum from Sunday is unlikely to carry over into next year. But Woods' win foreshadowed his improbable triumph at Augusta National Golf Club in the 2019 Masters.
The Masters remains the lone major to elude McIlroy. By adding a second Tour Championship trophy, the 30-year-old is positioning himself as the favorite for next year's tournament.