The 38-year-old, who took the Stonehaven Cup for a second time a fortnight ago when he prevailed at The Lakes by a shot, triumphed on the first extra hole at Coolum.
The lefthander closed with a five-under-par 67 to finish on 12-under-par 276. That total was later matched by Allenby who shot a 68 and Fraser after his 69.
Australian’s Adam Scott and Aaron Baddeley finished in a tie for fourth two shots shy of the playoff in the season-ending event on OneAsia. Scott fired a 68 while Baddeley carded 72.
Third round leader Kim Kyung-tae returned a 76 to finish in a tie for sixth. The Korean could have claimed the OneAsia Order of Merit title by finishing first but a four over par front nine proved costly.
The result meant that Australian Andre Stolz, who finished the tournament in a tie for 19th on five under par, secured the Merit crown with Kim ending in second place.
After they finished at 12 under par and then had to wait more than 30 minutes while the final groups completed their rounds, it was Chalmers who showed the most composure at the 18th when he safely found the fairway with his tee shot and then two-putted for par to take the Joe Kirkwood Cup.
Fraser dunked his tee shot in the water and eventually settled for a bogey after failing to chip in from the greenside bunker while Allenby went way right with his first shot, found the heart of the green with his third and then had to hole a four-metre putt to stay in the hunt but couldn’t do so.
“I was surprised to see that par was good enough, I thought we were going to have to birdie this hole but that’s how it goes sometimes in playoffs," Chalmers said.
Chalmers, who also won the 1997 Australasian Players Championship and boasts two Nationwide Tour wins, was steady rather than spectacular throughout the week, apart from the hole in one he produced on the opening day.
Having gone out in 35 with two birdies and a bogey on Sunday, spectacular he was after the turn as he picked up further shots at 10, 12, 16 and 17 to capitalise on faltering rivals.
But he didn't have to wait long to discover the title would not be his in regulation, with Allenby overcoming two bogeys on the front nine to collect three birdies coming home, before Fraser shrugged off bogeys at the 1st and 11th to make three critical birdies of his own in his last eight holes.
“I felt fine on the tee shot but the putt was the hardest thing. This Australian PGA Championship has such a rich history and to have won it now, coupled with the Australian Open, I’m over the moon,” added the Australian.
Kim led by four shots after starting with four pars but the wheels came off when he had two unplayable lies at the fifth and went on to make double bogey seven.
Nevertheless it was an outstanding season for the Korean who claimed the GS Caltex Maekyung Open in Korea.
It was a performance surpassed only by Stolz who tasted victory in the season-opening Indonesia PGA Championship and the Thailand Open.
The new season on OneAsia starts in 2012 with the Qualifying School in January.
Places on OneAsia in 2012 will be highly sought after as the schedule, which will be announced soon, will boast at least 12 tournaments offering an overall purse of US$15 million.
The Australian PGA Championship presented by Coca-Cola was joint sanctioned with the PGA Tour of Australasia.
