MacIntyre posted an eight-under 62 at Caves Valley Golf Club to take a three-stroke lead over Englishman Tommy Fleetwood into Friday.
Scheffler at four-under 66 is alone in third after taking the clubhouse lead earlier in the day.
Jason Day, Australia's sole representative in the tournament, is at two under.
The one-time world No.1 entered the tournament in 44th position in the FedEx Cup rankings, but with only the top 30 progressing to next week's Tour Championship he needs a high finish in Maryland.
Day made back-to-back birdies on the seventh and eighth holes before replicating the feat on the 14th and 15th.
Sitting comfortably at four under, and perched close to the top of the leaderboard, disaster struck when he made back-to-back bogeys on 17 and 18 to drop him down the leaderboard and six behind the lead.
His tie for seventh, however, sees him rise 15 spots in the standings to No.29, which will be enough as the end of the week to make next week's field.
MacIntyre, who entered the week 20th in the FedEx Cup standings, didn't believe a 62 was likely for anyone on Thursday.
"There's chances. If you drive the ball well, it does give you chances," the 29-year-old said. "... I'm sure the next couple of days won't be as easy."
MacIntyre birdied the 11th hole but bogeyed the 12th to sit at two under for his round. His remarkable birdie run began with a 66-foot putt at the par-3 13th and a 40-footer at No.14.
In fact, the first five birdies of that streak all came from at least 11 feet out. At No.18, he knocked his approach shot to inside five feet for the exclamation point.
"Probably the last six holes is probably as good as I've ever putted in a stretch of holes," said MacIntyre, whose big moment this year was a runner-up finish at the US Open. "Just so consistent."
Fleetwood's bogey-free 65 included a long putt of his own, a nearly 34-foot left-to-righter on the final hole to move past Scheffler for second.
"To go bogey-free around there is really, really good," said Fleetwood. "I think I made like two or three really good par saves, but apart from that, I did a lot of things well."
Fleetwood nearly captured his first PGA Tour victory last week at the FedEx St. Jude Championship but a late bogey kept him out of a playoff eventually won by countryman Justin Rose.
There was a two-hour, 13-minute delay in the afternoon due to lightning in the area. When play resumed, Scheffler birdied three of his final four holes to set the early pace at four-under 66.
"Significantly softer," Scheffler said of how the course changed. "The fairways were really rolling out to start the day. Greens were firm. So yeah, golf course changed pretty significantly after the delay."
Tied at three-under 67 are Rickie Fowler, Ben Griffin and Norway's Viktor Hovland.
Hovland, the 2023 BMW and FedEx Cup champion, needs a strong week to stay inside the top 30; he entered at No.28.
with AAP
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