World number three McIlroy, who is ninth in the FedEx Cup standings ahead of next week's Tour Championship in Atlanta, avenged Thursday’s costly triple bogey six at the 15th by making a two yesterday before chipping in at the 18th for birdie and a second successive 68.
"I probably didn't play quite as well today as I did yesterday but ended up shooting the same score," said McIlroy, who was tied fifth on six-under, just two shots behind clubhouse leader Adam Scott. "I'm probably coming off the golf course a lot happier than I was last night after dropping a few in last few holes and today picking a couple up."
He might have gone far lower but the four-time major winner was still pleased as the course becomes firmer and most testing.
He dropped an early shot at the 185-yard second, pitched to four feet to birdie the par-five third, missed a 12-footer at the fourth, rolled in a 17-footer at the sixth, missed from nine feet at the seventh, but then made a 20-footer at the eighth to get to five-under.
After failing to birdie the par-five 12th and three-putting the par-five 14th from 52 feet for bogey, he hit a high draw with a six-iron inside four feet at the 15th to improve by four shots on his first round score before chipping in from 30 feet for a closing birdie.
“It was just a really nice yardage," McIlroy said of his two at the 15th. "I bounced back well. I made an early bogey, was able to bounce back after that, made a bogey on the par-5 14th, bounced back with two nice birdies in the last four holes. It's getting tricky. It's getting firm. It's only going to continue to get that way over the weekend, so it's nice to be in position.”
As Scott doubled bogeyed the 17th and shot 69 to lead by one stroke from Scottie Scheffler and Cameron Young on eight-under, 37th-ranked Shane Lowry kept his chances alive of making the top 30 who qualify for the final counting Tour Championship with a level par 71.
The Offaly man was tied for 10th, just three shots off the pace on five-under and projected to move to 28th in the FedEx Cup while playing partner Séamus Power, 36th in the FedEx Cup, carded a three-under 68 to move to 22nd on three-under and to 35th in the projected standings.
On the DP World Tour, Ardglass' Cormac Sharvin (29) made his first cut since the Magical Kenya Open in March when he made five birdies in a three-under 69 to share 35th on four-under-par in the D+D Real Czech Masters at Albatross Golf Resort.
The former Walker Cup star, who had missed his last 13 cuts on the spin, trails Malaysia's Gavin Green by 10 strokes with Dubliner David Carey tied 48th on three-under after a 70.
The Island's Gavin Moynihan missed the two-under par cut by two strokes after a 73 as Greystones' Paul Dunne came up six shots shy after following a 76 with a 72.
Meanwhile, host Paul McGinley heads into the final round just one stroke behind leader Steen Tinning in the Irish Legends presented by McGinley Foundation at Rosapenna Hotel & Golf Resort.
In difficult conditions at the Old Tom Morris Link, McGinley and Italy's Emanuele Canonica carding one-over 72s to share second, a shot behind Tinning, who also shot 72, on one-under.
In the Challenge Tour's Dormy Open, Kinsale's John Murphy made seven birdies in a four-under 68 to move up to 20th on four-under, seven shots behind Finland's Lauri Ruuska in Stockholm.
Paul McBride took seven at the par-five 18th to miss the cut by a shot after a 77 as Tom McKibbin shot 74 and Ruaidhri McGee a 76 to miss out on three and four-over respectively.
In the 112th Irish PGA Championship, Carlow's Damien McGrane and North West's Brian McElhinney head the field by two shots heading into the final round at Carne Golf Links' Wild Atlantic Dunes Course.
Two-time champion McGrane shot a three-under 69 and McElhinney a 70 to lead by two strokes on five-under-par from 2013 champion Michael McGeady, who also shot 69.
Glasson's Colm Moriarty shot 72 and Neil O'Briain a 74 to trail McGrane and McElhinney by just four strokes on one-under.
On the PGA Tour Champions, Darren Clarke shot a seven-under 65 to share the lead with Jim Furyk and Vijay Singh in the Dick’s Sporting Goods Open at En-Joie in New York, one shot clear of Pádraig Harrington.