The 22-year-old South African finished on 14-under-par for a four-round total of 266 on Sunday after carding a final round of 67 at Stellenbosch Golf Club, a victory that also earned him qualification for next month's Masters in Augusta.
There was a three-way tie for second place with South Africa's Hennie du Plessis, Francesco Laporta of Italy, and Frenchman Frederic Lacroix all finishing on 269.
Jarvis was one stroke ahead at the start of the final round, but a birdie on the first hole meant he extended his lead and then tenaciously held on, even when play was suspended for 35 minutes because of thunder and lightning with a single hole left to complete.
Jarvis is the eighth-straight home winner of one of the oldest national open golf championships in the world, which was first played in 1903.
Last week, Jarvis won the Kenya Open in Nairobi by three shots, with Du Plessis finishing third and Laporta fourth.
He rolled in four birdies and a bogey in his final-round and made light of having to endure the delay as he stood at the final tee.
"I feel on top of the world in this moment. I feel absolutely incredible," he said afterwards.
"To win in front of my home crowd in my home Open is just absolutely fantastic, I've got no words!"
Australian Jason Scrivener ended up with a one-under 69 to finish on four under, leaving him tied for 24th place.
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