Van Rooyen, 29, who finished runner-up in Qatar and Morocco this season, stretched the lead to three strokes on the back nine at Hills Golf & Sports Club in Gothenburg.
Fitzpatrick, the 2016 champion, stepped up the pressure with a birdie-birdie finish to sign for a six-under-par 64 and when Van Rooyen bogeyed the 17th hole, the players were tied at 18-under overall.
But Van Rooyen made a gutsy birdie at the par-five 18th to take the victory and continue an impressive first year on the tour.
The result moves him inside the top 10 on the Race to Dubai rankings.
“It’s too good, it’s hard to describe,” he said. “I was so nervous on 18. On 17 I was fine, I just didn’t hit that putt hard enough and then I asked (caddie) Alex, ‘what are we at?’ and he told me that Matt went birdie-birdie.
“I’ve been putting so well all day and to hole that one to win my first one is pretty cool.”
Home favourite Henrik Stenson thrilled the fans with a hole-in-one at the sixth in a final round 66 that moved him up to third at 14-under alongside South African Dean Burmester, who carded the same score. (Reporting by Hardik Vyas in Bengaluru Editing by Ian Chadband)
