McIlroy failed to take advantage of four birdies in his first seven holes but still shot 69 to share second with Ryder Cup team-mate Tyrrell Hatton on eight-under, just a shot behind leader Antoine Rozner, who shot 65.
But Lowry is just three behind, tied for fifth, as he aims to round off a consistent year with a win.
“I knew I needed to go out and shoot a decent score if I wanted to get myself back in the tournament, and I did that,” Lowry said. “Hopefully, I can keep it going.”
McIlroy is confident he can add to his sensational record at the Earth Course and claim a third win in the season-ending event to wrap up his sixth Race to Dubai title.
“Look, my comfort level around this place, it’s always been there ever since the first time we played back in 2009,” McIlroy said. “But the course is set up different. I need to do a better job of hitting the fairways.”
McIlroy struggled with his driver mid-round but feels confident he can get the job done if he avoids the heavy rough.
“Look, I’m so comfortable around this place and I’ve had success before. So I’m liking my chances going into the weekend.”
Tom McKibbin was also upbeat, but with Rozner projected to leap to first in the battle for those 10 PGA Tour cards, McKibbin fell to 12th despite carding a 70 that left him tied 16th on three-under.
“We’ll try and tidy up a few things, but overall, I’ve been pretty happy to shoot two rounds under par so far,” McKibbin said.
At the PGA Tour’s Butterfield Bermuda Championship, Séamus Power carded a bogey-free, three-under 68 to dip inside the projected cut line at Port Royal.
He’s 54th in the FedEx Cup Fall Series with those ranked 51st to 60th after next week’s final event, the RSM Classic, guaranteed Signature Event starts in the AT&T Pebble Beach Pro-Am and Genesis Invitational next year.
He was eight shots behind Robby Shelton who posted a 64 to lead by one stroke in the clubhouse from Sam Ryder, who shot 62, on 10-under.
Meanwhile, Liam Nolan (T3), Marc Boucher (T18), John Murphy (T26) and Michael Young (T30) earned full cards awarded to the top 35 and ties at the Final Stage of the Alps Tour Qualifying School in Italy as Hugh Foley (T61) earned a Category 8 card.
