The Northern Irishman – and defending FedEx Cup champion – entered the day tied for eighth on nine under.
Weather delays led to a stoppage of almost two hours and as Xander Schauffele moved within three shots of Viktor Hovland’s 24-under lead through the 15th hole at the top of the leaderboard, McIlroy wrapped up on an impressive five-under round of 65 and 14 under overall.
His round at East Lake also featured birdies on the fifth, eighth, 12th, 13th and 15th holes.
Under the FedEx Cup ranking format, McIlroy started third, six shots behind Scottie Scheffler.
Over the weekend he told Sky Sports his post-Tour Championship focus would be “on getting myself right” ahead of the Irish Open at The K Club then BMW PGA Championship and Ryder Cup.
He told Sky Sports: “Yeah, there’s still quite a lot of golf to play...I guess next week will just be focused on getting myself right, some treatment, probably a little bit of time in the gym doing some rehab exercises and just making sure that I’m 100 per cent ready to go for Irish Open, then Wentworth, and then obviously we’ve got another week and then the Ryder Cup.
“I’m not too concerned that it’s going to give me any bother over the next few weeks, I’m glad that it’s started to settle down.
"So it’s a shame that it happened this week and I haven’t really been able to get the best out of myself.
"But I’m pretty confident that I’m going to be in a good spot for the next few weeks in Europe.
“I’m obviously not going to rush it...hopefully by the end of next week and by weekend going into the [week of the] Irish Open I’ll be back to feeling 100 percent again.”
The Horizon Irish Open will run in County Kildare from September 7-10.
McIlroy heads to Wentworth in England for the BMW PGA Championship across September 14-17.
Then it is off to Italy for the Ryder Cup from September 29 to October 1.