The Northern Irishman birdied the fourth play-off hole – the par four 16th – to edge out American and final round playing partner Ryan Moore in a thrilling finale to the PGA Tour season.
The four-time major winner shot a final round 64 to edge into a sudden death play-off with home favourites Moore and Kevin Chappell, who was eliminated after only parring the first play-off hole.
Moore, who had also shot 64 in normal play, holed a clutch birdie putt on the opening extra hole before Mcilroy missed an eight foot eagle putt for the title. The pair then halved the next two holes in par as the light faded in Atlanta.
It came down to the 16th, which Mcilroy had eagled in regulation after holing his second shot from the fairway. Moore looked to have finally cracked but held firm by holing a 25-footer for par before the European Ryder Cup star stepped up and rolled in a birdie from 15 feet to take home the lucrative spoils.
For much of the day it looked as though points leader entering the week Dustin Johnson would limp over the line after a closing 73 saw the 54-hole leader drop out of contention for the tournament.
It left the three-time Tour winner this year watching on nervously, hoping compatriot Moore could prevent McIlroy from sneaking in under the radar.
Johnson would still have claimed the overall title had Moore or Chappell triumphed in Atlanta by virtue of the fact they were not able to overhaul the 2016 US Open champion’s points lead at the top of the standings.
Mcilroy’s victory was his third of the year and second in three starts after claiming the Deutsche Bank Championship in Boston three weeks previously. England’s Paul Casey ended a strong season with a closing 64, and despite being a factor for most of the week, ultimately fell short of his goal and finished fourth on nine under par.
Defending champion Jordan Spieth surrendered his trophies relatively meekly, finishing with a two under par 68 for an even par total and a tie for 17th. Phil Mickelson, who admitted he used the week at East Lake to prepare for the start of next Friday’s Ryder Cup, came home in 29 for a round of 66 and a one over total in 22nd place.
The Tour and indeed the world of golf now turns its attention to Minnesota and the Ryder Cup, to see if team USA can regain the title it last won against Europe in 2008.
Home captain Davis Love III will name his fourth and final wildcard pick overnight and after electing to implement a rule allowing himself to complete his team after the conclusion of the TOUR Championship, it remains to be seen if he will be left looking sheepish having prematurely chosen someone other than Moore for the three days of play at Hazeltine next weekend.
TOUR Championship Final Leaderboard (East Lake Golf Club, Par 70) *US unless stated
-12** RORY MCILROY (NIR)
-12 Ryan Moore, Kevin Chappell
-9 Paul Casey (ENG)
-6 Hideki Matsuyama (JPN)
-5 Dustin Johnson
-4 Adam Scott (AUS), Jason Dufner
-2 Si Woo Kim (KOR), Charl Schwartzel (RSA), Bubba Watson, Emiliano Grillo (ARG)
E Jordan Spieth
+1 Phil Mickelson
+2 Russell Knox (SCO)
Final FEDEX CUP standings
1, Rory Mcilroy (NIR)
2, Dustin Johnson
3, Patrick Reed
4, Adam Scott (AUS)
5, Paul Casey
6, Jason Day (AUS)
7, Ryan Moore
8, Kevin Chappell
9, Jordan Spieth
10, Russell Knox (SCO)
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