Scheffler, who started the day with a five-shot advantage, carded a one-under 69 at East Lake to move to 13 under for the tournament, with world No 1 Jon Rahm his nearest challenger after a 65.
The American birdied two of his first three holes and added another at the ninth to reach the turn in 33, only to drop a shot at the 12th and see his lead cut to three when Rahm matched his birdie at the 13th.
Scheffler responded with a birdie at the 15th to restore his cushion, before closing with three pars in a row to stay clear at the top of the leaderboard heading into the weekend.
Rahm’s bogey-free 65 saw him reach nine under and pull clear of the chasing pack, with Bryson DeChambeau moving into third spot on five under after a five-under 65.
Justin Thomas is a further stroke back after a three-under 67, with defending champion Patrick Cantlay remaining at three under following a level-par 70.
The weather delay meant half the field did not complete their second rounds, with the second round set to be completed on Saturday morning before the third round gets underway.
The FedExCup winner will secure a $15m bonus, with Scheffler currently in pole position to claim the season-long prize.