The 29-year-old Scotsman, who shot a career-best 62 on Thursday capped by six consecutive birdies, added another six birdies in round two to reach 14-under 126 at the halfway stage of the second FedEx Cup Playoffs event at Caves Valley near Baltimore.
For MacIntyre, runner-up at June's US Open, this marks his lowest 36-hole score to par in a PGA Tour event - three strokes better than his previous best set at Myrtle Beach last year.
"Great two days' work," MacIntyre said. "If you leave yourself in the right positions you can be aggressive with the putts... I feel like my iron play has been top drawer this week and just continue to do that."
"I've been working hard," he added. "I've been putting really well for a long time now. It was just finding the confidence in the tee to green game and I feel like I've done that."
Scheffler, the season's points leader, followed with a bogey-free 65 - his 13th such round this season, the best on tour - and sits alone in second on 131.
"It was nice to have a clean card today, no bogeys," Scheffler said. "Did some good things out there. Five shots back going into the weekend is not too bad with the way Bob is playing right now. Did a good job to keep within shouting distance of him."
Sweden's Ludvig Aberg also impressed, birdieing three of his final five holes for a 64, placing him at 132, one shot ahead of Japan's Hideki Matsuyama. England's Tommy Fleetwood joined Americans Maverick McNealy and Michael Kim on 134, two further back.
Matsuyama matched MacIntyre's round with a bogey-free 64 of his own, birdieing four of his last eight holes to reach 133. Fleetwood, by contrast, slipped back with a 69 and now trails by eight shots.
Meanwhile, world No. 2 Rory McIlroy carded a 66 to sit at 136, tied for 11th and 10 strokes off the lead.
"I just want to try to play a good weekend and feel a little bit better about my game going into the Tour Championship," McIlroy said.