The 20-year-old had his four-shot halfway lead trimmed as he followed his 10-under 61 on Friday with a 67 at Vidanta Vallarta on Saturday to be at 20 under, with American Brian Campbell (64) snapping at his heels.
Potgieter was leading by three shots with two holes left when he badly missed his tee shot to the right on the par-3 17th and battled to save bogey.
Campbell finished with his seventh birdie of the day to be two shots clear of third-placed Stephan Jaeger of Germany, who posted a 66.
Australian veteran Aaron Baddeley was tied 22nd at nine under after a 68 while compatriot Karl Vilips (76) was equal last at two over a day after making the cut with a second-round 65 in his debut as a tour member.
Potgieter would love nothing more than a return to Augusta National, where he played in 2023 as the British Amateur champion.
He earned his PGA Tour card through his Korn Ferry Tour efforts, which featured one win early and a 59 in Colombia.
Firepower - particularly length - is what has kept him in front at Vidanta Vallarta, a course with five par 5s and plenty of room off the tee.
He has led the field in driving distance all three days, checking in 329.4 yards for his average on Saturday.
He played in the last group with Campbell and Jaeger — the same trio for the final round — and Campbell wasn't the least bit bothered by the difference in length.
Jaeger, who held off Scottie Scheffler to win the Houston Open last year, drove into the water on the reachable par-4 seventh hole after getting within one shot of Potgieter.
Alex Smalley had a 64 and was five shots behind, with Aaron Rai (68) and Ben Griffin (67) another shot back.
The stakes Sunday are more than just a trip to the Masters. The winner will gets in The Players Championship and the PGA Championship, along with five of the remaining $US20 million signature events. Jaeger is already in from his top-50 finish in the FedEx Cup last year.
