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Karmis posted a one-under-par-71 for a four-day total of 21-under-par 267 to defeat Kruger by two strokes at the Orchid Country Club.
Kruger was tied for the lead after 10 holes but fell behind after two costly bogeys on holes 13 and 14.
This was Kruger's second runner-up finish this season as he closed with a 69 for a 269 total at the 400,000 dollar event.
Thailand's Pariya Junhasavasdikul (68) signed off with a 270 total to finish in third place, his best placing this season while Australia's Scott Hend (67) was two strokes back on 272 at the inaugural tournament.
Evergreen Mardan Mamat was the best local performer, finishing in tied fifth place with Taiwan's Chan Yih-shin and South Korean Young Nam on a 273 total.
"The first thing that comes into my mind is all the privileges that come from winning on the Asian Tour," said Karmis.
"The rest of my year is pretty much sorted out. It has suddenly changed from wondering if I could get into tournaments to getting into all the tournaments," he said.
Karmis, who earned his Tour card from the Asian Tour Qualifying School in Thailand this year, got off to a slow start after making the turn on even-par 37 and carding a bogey on the 10th hole. His round turned for the better when he birdied holes 11, 15 and 17.
"I actually hit good iron shots on the front nine but they just went long and I missed a couple of short putts. I was hitting the ball well and I would rate today as the best I have hit so far," he said.
" But I missed the greens by a fraction and had tricky chips," said Karmis, who won a cool 63,400 dollars with the title.
The South African, who endured a sleepless night yesterday, tipped his hat to his resilient compatriot.
"Jbe is a great player and he is such a fighter and never gives up ever." Kruger, who lost in a play-off to Bangladeshi Siddikur at the Brunei Open in August, had to settle for his second runner-up finish but was gracious in defeat.
"I feel I'm getting closer to victory and overall I'm happy with my performance and happy that Peter won. He played a great tournament," he said.
Final round scores:
267 - Peter Karmis (RSA) 63-63-70-71
269 - Jbe Kruger (RSA) 66-66-68-69
270 - Pariya Junhasavasdikul (THA) 66-68-68-68
272 - Scott Hend (AUS) 67-71-67-67
273 - Chan Yih-shin (TPE) 65-67-68-73, Mardan Mamat (SIN) 65-69-69-70, Young Nam (KOR) 70-69-65-69
274
- Gaganjeet Bhullar (IND) 67-65-70-72, Lu Wei-chih (TPE) 69-66-67-72,
Kim Felton (AUS) 65-67-72-70, S.S.P. Chowrasia (IND) 68-65-71-70,
Hirotaro Naito (JPN) 65-71-68-70, Unho Park (AUS) 67-69-69-69, Gavin
Flint (AUS) 68-68-69-69, Anirban Lahiri (IND) 69-66-73-66, Corey Harris
(USA) 67-71-70-66, Danny Chia (MAS) 69-71-68-66
275 - Choi Jin-Ho (KOR) 67-69-66-73, Matthew Rosenfeld (USA) 67-68-68-72, Kiradech Aphibarnrat (THA) 68-67-69-71
