With a glittering leaderboard featuring six Major winners and four players who have held the number one ranking packed into the top 10, McIlroy carded a five-under 67 at Crooked Stick Golf Club to collect his fourth US PGA Tour win of the season and second in seven days.
The mop-topped Northern Irishman finished 20 under par and will head to the September 20-23 Tour Championship in Atlanta as the favourite to walk away with the $10 million bonus that will go to the FedEx Cup points leader.
Former world number one Lee Westwood and four-times Major champion Phil Mickelson tied for second place at 18 under par.
"I just wanted to go out and play as best as I could," said McIlroy, adding he plans to go to New York next week to train with NBA side the New York Knicks. "I knew if I played to my ability that I would win events.
"I didn't think that everything would happen so quickly, but I'm just on a great run at the minute and trying to keep that going for as long as possible."
If there was any doubt, the victory over the all-star line-up confirmed McIlroy's status as golf's dominant player.
He becomes the first golfer since Tiger Woods in 2009 to win US PGA Tour events on back-to-back weeks and joins Woods and Jack Nicklaus as the only players since 1960 to win six US PGA Tour titles before the age of 24.
With four US PGA Tour wins, including a second Major at the PGA Championship, McIlroy also moves into pole position to claim player of the year honours.
"Rory was putting on a show out there," praised Woods, who was partnered with McIlroy through the opening two rounds. "He's doing the things he needs to do and as he said, he's feeling very confident about his game.
"Right now, he's just really playing well and makes a ton of putts. That's a great combo."
McIlroy began the day a shot back of overnight leaders Mickelson and Vijay Singh, but was on the move quickly with birdies at the second and fifth before topping the leaderboard to stay with back-to-back birdies at nine and 10.
The 23-year-old then pulled away from the field with two more birdies at 15 and 16 to open up a three-shot cushion with two to play.
Mickelson, who has discovered a rich vein of form in recent weeks himself, tried to keep pace by trimming McIlroy's advantage to two with birdies on 15 and 16.
But a bogey on 17 removed any suspense, allowing McIlroy a leisurely stroll up the 18th where he signed off with his only bogey of the day, a small fist pump and a winning total of 268.
Mickelson returned a two-under 70 to finish joint second with Westwood who clinched his first ticket to the Tour championship with a three-under 69.
"I was a little bit off today, my timing was just a fraction off," said Mickelson. "But I'm really pleased with the way my game has come around the last two weeks.
"I had a fourth last week, tied for second this week.
"It puts me in a position where if I can improve just a little bit more for the Tour Championship and win, I'll be able to win the FedExCup."
Woods, who failed to qualify for the Tour Championship last year, is headed back to Atlanta's East Lake Golf Club with an eye on the collecting the $10 million prize for a third time after returning a three-under 68 to finish in a tie for fourth with American compatriot Robert Garrigus (69) at 17-under.
"It's getting better," said Woods. "I just need to (not) have that one little stretch of holes.
"That little stretch sometimes takes you out of a tournament, especially in a shootout like this."