Woods, a two-time winner of the tournament, carded six birdies in his opening seven holes during his third round, opening up a five-shot lead at one stage.
He eventually cooled off for a five-under 65 and a three-shot lead over McIlroy, who fired a four-under 66, and Justin Rose, who carded a 68, at the East Lake Golf Course.
Woods, the 14-time major winner, has the 54-hole lead for the first time since his last victory in 2013 at the Bridgestone Invitational.
Rory McIlroy will partner Tiger Woods in the final round
Rory McIlroy will partner Tiger Woods in the final round
He has never lost an official tournament when leading by more than two shots and has won 54 of the 57 PGA Tour events in which he has held the 54-hole lead.
Woods had started the day tied for lead with Rose on seven under par but made a blistering start. He set the tone by holing from more than 20 feet on the first hole and only a par on the second interrupted his stunning early birdie sequence.
He holed another lengthy putt on the fourth while his birdies on the sixth and seventh came after impressive shots out of bunkers.
There was a setback with a bogey on the ninth but that was cancelled out by another birdie at the par-four 12th.
At one stage he led by five from Rose but he dropped another shot after failing to chip up a slope to the 16th green. He got his second attempt at the shot close to the hole and took a bogey before finishing his round with successive pars.
Justin Rose remains in contention in his bid to claim overall FedExCup victory
Justin Rose remains in contention in his bid to claim overall FedExCup victory
Rose, who can win the overall FedExCup title with victory here, birdied the 16th and McIlroy gained two shots late in his round to cut the deficit but Woods remained in charge heading into the final round.
The American told Sky Sports: "There are some good guys behind me chasing, guys who have been playing well, and I've got my work cut out tomorrow."
Victory for Woods would cap a fine return to the top level this year following spinal fusion surgery in April 2017.
"This whole season has been pretty remarkable considering where I have come from," said Woods.