The 46-year-old Scott continued his vintage form with a second-round three-under-par 67 to climb into a tie for seventh at the $US40 million showpiece at East Lake.
A winner of the grand season finale 20 years ago, Scott will enter the weekend just three shots behind halfway pacesetters Ryan Gerard and Viktor Hovland after a tidy bogey-free round.
Scott will also start moving day with momentum after collecting his third birdie of round two on his very last hole.
Lee, though, will be eager to put his second round behind him as the 28-year-old strives to reignite his bid to become the first Tour Championship debutant since Xander Schauffele in 2017 to pocket the monster $US10 million winner's cheque.
After matching his career low round with a masterful 62 on Thursday, Lee stumbled with a horror triple-bogey seven on the par-4 fifth hole.
After spraying his drive into the right rough, the Australian No.1 needed two more shots to find the fairway, then three-putted to suddenly slip from eight to five under and back in the chasing pack.
Lee rebounded with his first birdie of the day on the next hole, only to drop two more strokes before signing for a three-over 73.
He is still in the mix at four under but will start the third round five shots behind, after being two in front before Friday's slip-up.
Cameron Young fired the day's low round, matching Lee's opening 62, to rocket from equal last to equal fifth.
"The field seems to be playing pretty well for even-par being last place after yesterday," said the reigning Players' champion.
"I can pat myself on the back for shooting eight under, but that doesn't change how much work there is left to even give yourself a chance."
Young has good reason to be cautious with world No.1 Scottie Scheffler moving ominously to eight under also, following up his first-round 65 with a 67.
But Gerard (65) and Hovland (66) are the new men to catch after reaching 10 under for the championship.
"It's a lot like the golf course that I kind of grew up playing in North Carolina," Gerard said.
"Feel very comfortable with the visuals, some of the elevation change, tee shots, and the greens are the same kind of Bermuda that I putt on at home."
Fellow Americans Chris Gotterup and Collin Morikawa are his closest challengers, one stroke behind after both carded second-round 67s.
Jacob Bridgeman (67) is tied 15th at five under after dropping a shot on the par-five 18th where his errant drive missed the fairway and found a pizza tent.
