After opening with four pars, Lowry – who has been without an individual victory since September 2022 – made back-to-back birdies on the fifth and sixth holes.
The former Open champion took a share of the lead with a run of five consecutive birdies starting at the par-four 11th before landing a shot at the last to edge Nakajima.
“It’s not that difficult when you’re hitting in play, but you start missing fairways, it gets pretty tricky, so I’m happy with that,” Lowry said.
He added: “You have to shape it around the course, hit it into position off the tee and it all depends on your iron play. It’s one of my strengths and I took advantage of that today and managed to sink a few putts on the back nine which was good.”
Lowry added that there had been a “little bit” of discussion about the Ryder Cup with playing partners Fleetwood and Donald.
“We could hear the horns from the road, it wasn’t as off-putting as Bethpage [Black] crowd,” he said with a smile, referring to the hostile New York fans at the Ryder Cup last month.
Fleetwood mixed four birdies, an eagle and two bogeys to find himself four shots behind.
Donald, playing his first tournament since his second Ryder Cup success as captain, made five birdies and a bogey to match fellow Fleetwood Englishman and 2023 Open champion Brian Harman.
Playing with McIlroy, American Ryder Cup player Ben Griffin opened with a 68 while McIlroy’s European teammate Viktor Hovland posted a 71.
