World number one Koepka nailed a magnificent approach shot to around one foot on the 18th, giving him a tap-in for birdie to complete a two-under-par 68.
Koepka's strong finish at the East Lake course left him on 15 under for the tournament, one clear of Rory McIlroy and Xander Schauffele.
The third round had resumed on Sunday after play was halted on Saturday as an electrical storm battered the course.
Six fans were hospitalised shortly after play was suspended when lightning struck a tree near the 16th tee.
The fourth round will get under way as scheduled later Sunday with Koepka in pole position to claim the $15 million jackpot on offer to the winner of the PGA Tour season finale.
England's Paul Casey is four off the lead on 11 under alongside Justin Thomas, whose challenge faltered with a one-over-par 71 on Sunday.
Three players -- Hideki Matsuyama, Jon Rahm and Chev Reavie -- are tied for sixth place, nine adrift of Koepka on six under.