The 27-year-old American carded a two-under 68 in the final round at the East Lake Golf Club to finish at 11 under and clear of countryman Jim Furyk and world number one Rory McIlroy.
Victory in Atlanta made it back-to-back wins for Horschel, who was nerveless as he took out the $10million FedEx Cup bonus.
After claiming the BMW Championship, Horschel predicted another win would follow and he was proved right as he grabbed his third PGA Tour victory.
Furyk (69) finished at eight under alongside Northern Irishman McIlroy (71).
Horschel shared the overnight lead with McIlroy, and his putter set him up on the front nine on Sunday.
A 10-foot birdie putt on the fourth and an 18-footer at the fifth saw him to two under for the day.
Horschel bogeyed the 10th but made up that shot at the 15th, and he was fired up after a 30-foot par putt at the 16th.
With Furyk dropping a shot at the 18th, Horschel carried a three-shot lead into the final hole and made an easy two-putt par to complete his win.
McIlroy endured a difficult day as a double bogey and bogey on the front nine proved costly.
He made back-to-back bogeys to start the back nine before finding some form with a hat-trick of birdies that ultimately came too late to leave him third in the play-offs.
Furyk made three bogeys, including two on the final two holes, as he remained winless this year and finished fourth in the FedEx Cup.
American Chris Kirk (68), who finished second in the play-offs, Englishman Justin Rose (69) and Australian Jason Day (69) were tied for fourth at seven under.
Ryan Palmer (69) was outright seventh a further shot back, while behind him at five under was Rickie Fowler (71).
Australian Adam Scott (70), Spaniard Sergio Garcia (66) and American Gary Woodland (67) were tied for ninth at four under.