Scott, a winner at the WGC-Bridgestone Invitational last month and a Top-10 finisher at the PGA Championship, shot a 5-under-par 65 at the East Lake Golf Club to complete 36 holes at 8-under 132.
Scott entered the Tour Championships in 19th place in the year-long points race that will determine the winner of the FedEx Cup and its top prize of $10 million. If the current standings hold through Sunday, Scott would vault all the way to first place.
First-round leader Keegan Bradley was among those tied for fifth at 135. Webb Simpson, who came into the tournament leading the FedEx points list, was tied for 19th at 139.
Scott played the first six holes in 2-over, but began a sizzling stretch of golf with a birdie at the par-4 seventh. That was the first of four straight birdies for Scott, who also birdied the final two holes.
"I was pretty annoyed at myself [because of his start], but I'm playing too good to let myself slip away at the moment," Scott said.