Villegas made par on the No. 18 at East Lake Golf Club while Garcia bogeyed the hole after finding the rough and bunker on his first two shots.
Villegas shot 4-under 66 and Garcia had 71 to finish at 7-under 273 after 72 holes, a shot ahead of Anthony Kim (69) and Phil Mickelson (69).
Vijay Singh will take home FedEx Cup title after shooting 70 in the final round to tie for 22nd at 9-over 289. The Fijian took a commanding lead in the golf’s four-week playoffs by winning the first two events.
Villegas, who won the BMW Championship earlier this month, finished second in the FedEx Cup standings. Garcia was third.