The 33-year-old overturned Scottie Scheffler’s six-shot advantage to finish one ahead of both Sungjae Im and the American.
McIlroy, a four-time major champion, shot a four-under 66 to finish one stroke ahead of the world number one and the South Korean on 21 under.
The prize money for McIlroy’s victory at East Lake, his fifth championship of the year, is $18 million (£15.36 million).
McIlroy told Sky Sports, “What a week, what a day.
“Scottie deserves at least half of this, in my opinion. He is a fierce competitor. It was an honor to fight beside him.
Scheffler entered the week with a six-shot lead over McIlroy as players began the season-ending tournament on staggered scores based on their individual places in the FedEx Cup standings.
Lightning forced the third round of play on Saturday to be postponed, and when play resumed on Sunday morning, 26-year-old Scheffler led by only one stroke. However, when the final round started later that day, he had increased his advantage to six strokes.
In their final rounds, the duo bogeyed the first hole, and Scheffler, who was feeling off, made more errors on the fourth and sixth holes.
McIlroy, on the other hand, rebounded from his initial bogey with a birdie on the third and three more birdies in a row starting from the fifth.
That established the tone for the day, and by the time they reached the 18th tee, McIlroy had a one-shot lead. The PGA Tour season came down to the last hole.
Both players struck solid drives, but McIlroy, who had been playing with dominance all day, pulled-hooked his approach shot and could only manage a par five.
However, Scheffler was unable to profit from the situation. Hitting the last of many mediocre bunker shots, the Master’s winner barely parred the final hole to record a dismal 73.
He tied for second place with 24-year-old rising sensation Im, who shot 66 and had a chance to win the tournament.
“When I hit the tee today, I didn’t give myself much chance. I anticipated it would be challenging to catch up after falling six shots behind, but with my strong play and Scottie’s poor performance, the game was still in play heading into the last nine holes, according to McIlroy.
McIlroy has been one of the PGA Circuit’s most significant figures in the continuing power struggle in golf, and he was at one of the meetings earlier this month when the top players on tour discussed the danger posed by LIV Golf.
After his victory, he declared: “I believe in the game of golf, in this circuit specifically, and in the players on this tour.
“I’ve played golf all over the globe, and here is the best spot in the world to do it.
“This is a time in which I am tremendously pleased, but it should also be a one in which the PGA Tour is incredibly proud. They have had some hardship this year, but we are persevering, and today’s display was impressive.
“I hope everyone at home enjoyed seeing two of the top golfers in the world battle head-to-head for the highest reward on the PGA Tour.”
After being eliminated from the 150th Open Championship, when he shared the lead after 54 holes but placed third behind Australia’s Cameron Smith, McIlroy claimed the FedEx Cup triumph would “soften the blow.”
For me, St Andrews was quite challenging. It was difficult to overcome,” he remarked.
“This somewhat lessens the blow. Even while it doesn’t make things any simpler to overcome, closing the season on this positive note is fantastic.