Bidding for a victory that would give him his fourth FedEx Cup, the Holywood star thinned his third from a bunker over the 18th green as officials prepared to sound the horn to suspend play due to approaching storms.
But he was happy to see it rebound off the hospitality tent to 17 feet from where he rolled in the birdie putt for a four under 66 that left him joint eighth, just five shots behind leader Russell Henley and only three behind playing partner Scheffler, who shot 63 to sit alone in second.
World No. 1 Scheffler admitted later he was pulling for McIlroy as he feared they wouldn’t have finished had the Down man been forced to take relief.
He was two shots behind Henley, who took advantage of preferred lies at a rain-softened East Lake to shoot a brilliant 61.
McIlroy felt he deserved to shoot 66 at worst, even though he three-putted the 14th and made a soft bogey at the 16th.
“Yeah, pretty lucky in the end,” he admitted after a day where he kick-started his round with an eagle at the sixth and sprinkled in four birdies.
“I think as well, if it hadn’t have come down (off the tent) and we had to drop, we mightn’t have got finished, so lucky in a lot of different ways, lucky for the score and lucky we got done.
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“I feel like I played well enough to shoot four under if not better, so it was a nice and lucky way to finish.”
The world number two admitted his first thought was “Oh, no,” as he thinned his long bunker shot at the 18th.
“Got it a little thin, came out a little faster than obviously I wanted it to, but at that point you’re just hoping that something is going to happen — all the TIO (Temporary Immovable Obstruction) lovers are going to love that one on Twitter tonight.”
As for the rest of his round, he was happy.
“I felt like I drove the ball a lot better than I did last week, so that was a big improvement,” he said. “Honestly, my iron play, I struck the ball much better. I sort of shook a lot of rust off last week, and I felt like I was going into this tournament a better golfer than I was last week.
“Still didn’t feel like I got the most out of my round; a three-putt on 14 and then the bogey on 17. But overall, I played much better than last week, which was a positive.”
Henley took advantage to make over 200 feet of putts and lead by two strokes from Scheffler and by three from European Ryder Cup qualifiers Robert MacIntyre and Tommy Fleetwood, and US wildcard hopefuls Collin Morikawa, Patrick Cantlay and Justin Thomas
The winner of the Tour Championship will win the FedEx Cup, and Scheffler remains the favourite after a round where he made seven birdies and a key par save from 27 feet at the 16th before finishing with two birdies
Shane Lowry fought a lukewarm putter and made two birdies and two bogeys in a 70 to share 23rd on level par.