Defending champion Scott - winner of last year's event ahead of four others including Tiger Woods - carded a scintillating six-under-par 65 to be a stroke clear alongside American Cameron Tringale at the Ridgewood Country Club.
Scott - 15th in the rankings - opened his FedEx Cup play-offs campaign in New Jersey with a two-under first round on Thursday but the Australian stepped it up a notch on day two as he overturned a four-shot deficit to move level at the top of the leaderboard at eight under through 36 holes.
The world number two was set up by a near-faultless front nine, with four successive birdies approaching the turn.
Scott started the round with a birdie at his first hole, before he dropped a shot at the par-five third.
That was the only blemish on Scott's round as the 34-year-old went on a run of birdies, holing four in a row starting at the fifth hole, including a 21-foot putt at the eighth.
He added another two birdies on the back nine, with the highlight being his 156-yard approach to within a foot of the 18th hole as he ended the round alongside Tringale.
Tringale - 61st in the FedEx Cup rankings - had a bogey and a double bogey inside his first three holes on the back nine but he recovered with six birdies throughout for a second-round 68.
Scott and Tringale are a shot clear of American trio Kevin Chappell, Brendon Todd and Jim Furyk.
Chappell went bogey-free as he shot a four-under-par 67, while Todd and Furyk both had 69s.
Reigning FedEx Cup champion Henrik Stenson (64) headlines a group of six players tied for sixth spot at six under.
The Swede is joined by South African Ernie Els (68), first-round leader Bo Van Pelt (71), Scotsman Russell Knox (69), Australian Jason Day (64) and American Kevin Na (66).
Meanwhile, world number one Rory McIlroy recovered from a poor opening round to close to within five shots of the lead.
McIlroy was nine strokes off the pace at the start of play but a blemish-free round, which included six birdies, saw the Northern Irishman rocket into contention.