The 17-year-old secured a nailbiting 3&2 victory over the Englishman in Saturday's 36-hole final to become the youngest winner since Matteo Manassero's 2009 triumph aged 16.
A superb bogey-free, four-under-par 66 in the morning session gave Potgieter a seven-hole lead only for Bairstow, 23, to battle back to two down with four to play.
There were echoes of Laird Shepherd’s comeback from eight down at Nairn in last year's final but Potgieter displayed a maturity beyond his years and an exceptional short game to seal the glory.
Potgieter, placed 140th on the World Amateur Golf Ranking, can now look forward to competing in The 150th Open at St Andrews next month, the 2023 US Open and, by tradition, an invitation to play in the Masters. The teenager will also be invited to play in an event on the DP World Tour.
He becomes only the third South African to win the event after Jovan Rebula at Royal Aberdeen in 2018 and Bobby Cole at Carnoustie in 1966.
From a record entry and a 288-man starting field last Monday, representing 42 countries, the finalists played out an epic contest.
But the Sheffield man made the more nervous start as bogeys on three of the first six holes left Potgieter, who birdied the third, four holes up.
After a delightful approach to the short ninth, the South African rolled in the short putt to extend that lead further.
Potgieter looked in trouble on the par-five 11th after pulling his drive but he drilled a brilliant, low approach and won another hole as Bairstow fluffed his chip.
The gap was seven after Bairstow bogeyed the 12th but only his second birdie of the day at 13 gave him hope.
The Hallowes member continued to battle, sharing the next four holes, but he was bunkered off the 18th tee and found himself seven down at halfway.
An errant tee shot from Potgieter at the 21st saw him make his first bogey, allowing Bairstow to win just his second hole.
Potgieter, a three-time winner at junior level in his homeland this year, hit another poor tee shot at the next only to rescue a half with a 10-foot putt.
Bairstow had renewed belief and holed a 35-foot putt at the 24th to spark a roar from the crowds, but a birdie at the 26th saw Potgieter reclaim a six-up lead.
Bairstow made another of his five birdies at the 28th and also won the 30th and 31st to move within three.
As Potgieter continued to find sand. Bairstow claimed a third successive hole at 32 only for a double-bogey at the 33rd to end his hopes as his opponent closed out victory with a par.
The top-level golf continues on the Fylde coast on Monday, with regional qualifying for The Open at Fairhaven followed by final qualifying at St Annes Old Links eight days later.