The 33-year-old from Northern Ireland fired a four-under-par 66 to finish on 21-under 263 at East Lake in Atlanta.
Four-time major winner McIlroy took the $18 million top prize in the season-ending playoff showdown by one stroke over reigning Masters champion Scheffler, who fired a 73 on Sunday, and South Korean Im Sung-jae.
“I feel like Scottie deserves at least half of this,” McIlroy said. “I feel sort of bad that I pipped him to the post.”
McIlroy, who has been a major advocate for the PGA Tour in its ongoing battle with the Saudi-backed LIV Golf Series, said it was more special to win this year in accepting the trophy.
“It means an awful lot,” McIlroy said. “I believe in the game of golf. I believe in this tour in particular. I believe in the players on this tour. It’s the greatest place in the world to play golf bar none and I’ve played all over the world.
“This is an incredbly 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’re getting through it.
“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.”
Fourth-ranked McIlroy won the 2016 and 2019 Tour Championship titles and roared back to win from 11 strokes back late in the second round and six shots down as the final round began.
McIlroy sank a stunning birdie putt at the par-3 15th from just inside 32 feet, the ball breaking to the left and dropping into the hole, to match Scheffler for the lead on 21-under.
McIlroy blasted out of a bunker way beyond the 16th green but pitched inside eight feet and made the par putt while Scheffler missed a par putt from just inside nine to hand McIlroy the lead.
Both parred 17 as the tension grew.
At the par-4 18th, Scheffler found a greenside bunker while McIlroy bounced his second shot off the left grandstand and into deep rough.
Scheffler went over the green out of the sand then pitched back onto the green while McIlroy chipped onto the green and two-putted for par and the victory.