The Offaly man turned in three under at Delhi Golf Club thanks to a 20-foot par save at the ninth.
But even after making some mental errors on the back nine, he birdied the last to card a three under 69 that left him alone in third on 14 under, just three shots behind the Japanese star.
“Yeah, I got very frustrated on the back nine today,” said Lowry, who bogeyed the 10th and followed a birdie at the 15th with a bogey at the next before finishing with a birdie.
“I started to hit very loose shots and made some silly mistakes. It was disappointing on the back nine.
“I played great on the front nine. I was really in control of my game and with how things were going.
“Made a great par save on nine and then I just missed a short putt on 10, and then it kind of snowballed from there.
“I did my best to get it back on track, and it was nice to birdie the last, but I made a couple of really silly mental errors, but it is what it is. I’m still only three back.
“Keita played great today, so he’ll be hard to beat tomorrow, but there will be a few of us not far behind him, hopefully giving him a run.”
Nakajima said he copied Lowry’s rhythmical swing to fire a bogey-free, seven-under 65 and lead by two shots from Tommy Fleetwood, who also shot 69, on 17-under.
“Ahead of tomorrow, yeah, I’ll be fine,” said Lowry, who will be looking to repeat the brilliance of his opening 64. “I’ll reset tonight and look at the leaderboard.
“I’m in a great position in this tournament. I like the golf course. I think it suits me, and I think I’ll have a low score out there.
“I’ve already shown that once this week. I’ll need a low one tomorrow to try and win.”
Indian Special Olympics athlete Ranveer Singh Saini and Rory Mcilroy
Rory McIlroy knows he will need something extraordinary to have a chance after a 68 left him seven behind Nakajima on 10 under.
“Yeah, still quite a bit back, depending on how the guys play the back nine,” McIlroy said after a five-birdie round that included his third bogey of the week at the 11th, where he couldn’t take advantage of a superb greenside sand shot.
“But I’d imagine that if I shoot a low one tomorrow, I could post a score and see what happens.
“But I’d say I’m probably two shots too far behind to have a realistic chance. But I could go out and shoot a low one tomorrow.”
At the HotelPlanner Tour’s Hangzhou Open, Max Kennedy needs a low final round to keep his hopes of a DP World Tour card alive.
A three over 75 left him joint 50th on three under and projected to fall from 45th to 47th in the Road to Mallorca standings.
Only the top 45 in the rankings after this week will contest the season-ending Rolex Grand Final in Mallorca, after which the top 20 in the final standings will be awarded DP World Tour cards.
Liam Nolan, who missed the halfway cut at Hangzhou West Lake Golf Club, was projected to fall from 37th to 43rd in the Road Mallorca.
Peru’s Julian Perico and Austria’s Lukas Nemecz share a one-stroke lead heading into the final round.
At the LPGA’s BMW Ladies Championship in Korea, local star Sei Young Kim leads by four shots from American Yealimi Noah and Japan’s Nasa Hataoka on 19 under.
Leona Maguire shot a bogey-free 69 to move to 52nd on three under.
