Donald began the day at East Lake tied for the lead with playing partner Jim Furyk and had ground out a one shot advantage after nine holes.
But the Ryder Cup wild card - playing his last event before next week's contest at The Celtic Manor Resort - then carded five straight pars before running up a double-bogey seven at the 15th.
"I was in pretty good shape after two shots but hit a horrible wedge (into a greenside bunker) and three-putted to easily rack up a seven," Donald admitted after carding a 71 to finish seven under par alongside Retief Goosen (66), one shot behind leader Furyk.
"I'll try to forget that and other than that it was a pretty solid day.
"I would rather be level with Jim than one behind, he's a very solid player, but it was one of those days where I had a few putts that hit the edge of the hole.
"But I am still in good shape."
Donald made the ideal start with a superb tee-shot and ten foot birdie putt on the par three second, but dropped a shot on the fifth.
A run of three pars were then followed by a birdie on the par five ninth and saw Donald reach the turn in 34 to lie nine under par, one ahead of Furyk who had carded nine straight pars.
The American then dropped a shot at the tenth but birdied the 14th and 15th before a bogey on the 17th reduced his lead to a single stroke.
Australian Geoff Ogilvy is three off the pace on five under after a round of 72.
Ogilvy appeared to be suffering the effects of barely any sleep after staying up to watch his beloved St Kilda in the AFL Grand Final when he bogeyed the first and ran up a double bogey on the second.
But the former US Open Champion hit back with birdies at the fourth and fifth to get back in contention and, after further dropped shots on the 13th and 14th, he finished in style with a birdie two on the 18th.
The winner of the tournament tomorrow will collect a first prize of £860,000, with the overall FedEx Cup champion claiming a bonus of £6.4million.