The Englishman missed a par putt on the 18th green at the Portugal Masters in November to lose his playing privileges by just 100 euros but was handed a reprieve when Patrick Reed opted not to play the Final Series.
He made the very most of his second chance at Glendower Golf Club, overcoming World Number Two McIlroy on the third extra hole after an enthralling closing round.
Storm hit his approach to the heart of the 18th and made his par three times in the play-off, with McIlroy missing the green at the third attempt and leaving himself an eight-foot putt for par that missed on the low side.
The 38 year old had entered the final day with a three-shot lead and got to 18 under with a closing 71 but McIlroy reeled him in with a 68 to set up the dramatic finale.
Englishman Jordan L Smith finished a shot out of the play-off after a 68, with Dean Burmester at 15 under, a shot clear of fellow South Africans Thomas Aiken and Trevor Fisher Jnr.
The win is Storm’s second on the European Tour and first since the Open de France ALSTOM, nine years and 198 days, and 274 events ago.
McIlroy was playing the event for the first time since 2009 after being drawn to Gauteng by tournament host and great friend Ernie Els, and the huge crowds that flocked to see him and the rest of the field on Sunday were treated to a wonderful spectacle.
McIlroy put his approach to five feet on the first and rolled his eagle putt to tap-in range on the par three second but Storm’s tee-shot on the par three third was to 12 feet and he was two ahead.
The Northern Irishman then birdied the eighth to keep the pressure on Storm who made smart par saves on the fifth, seventh and ninth.
McIlroy used his immense power to claim a simple birdie on the par five 13th and when Storm produced a nervy three-putts from the fringe on the 14th for a first bogey in 55 holes, the 27 year old had the lead.
Storm and McIlroy both made birdies on the par five 15th but when McIlroy found a horrible lie in a greenside bunker on the 17th, he made a bogey after failing to get out, sending the two into the play-off.
Regulation pars were the order of the day on the first trip up the 18th while McIlroy had to produce a brilliant low hook from the trees after a poor tee-shot to make his par the second time around.
Smith had bogeyed the first but he made an eagle from 15 feet on the second and birdies on the third, fourth and sixth had him one off the lead. A double-bogey on the seventh stalled the 2016 Challenge Tour number one’s progress but he made a birdie on the eighth to stay in touch.
A beautiful approach was helped by a nice bounce to set up a second eagle on the 15th before he bogeyed the 17th on his way to finishing third in just his fifth European Tour event.
European Tour Release