The 27-year-old hit a final round five-under-par 67 for a 15-under par total in the Asian Tour event held at the Royale Jakarta Golf Club.
Open champion Els carded a 68 to finish second, while overnight leader Daisuke Kataoka of Japan slipped back to third, a shot further back after a final round 70.
"I was struggling in the beginning after my birdie on one. But at the turn, I got a bit of momentum going because I was confident with my ball striking," Wiesberger said after claiming his fifth professional victory.
The Austrian took the lead from Kataoka with an eagle-three on the par-five 12th only to see playing partner Els match his score to keep up the pressure.
"It was good to hole the eagle and it was nice that Ernie stayed in touch. He wouldn't let go and that's why he is such a great champion. It was a good time to do that and it got my round going," he added.
Els, whose lone bogey of the round came on the fifth hole, was not too dissatisfied with his week's work.
"I played and fought hard. I wasn't quite at my best but had a good time. I didn't hit my iron shots close enough especially at the start. I was one over through five holes and had to battle back all the time," Els said.
"A win would have been unbelievable but second is not all that bad. This has given me something and it shows my game is going in the right direction. I'm starting to feel really good about my game.
"I think Bernd played better than all of us. I played with him for three rounds and I think he deserves to win."