'My biggest problem was getting ahead of myself today,' said Allan, who played on the PGA Tour in 2002. 'A couple of times I looked at the board, I was trying not to look at them but I couldn't help it. After that, it probably helped me knuckle down and keep my focus.'
Allan finished the tournament at 12-under-par 198 and won by a single stroke over some highly regarded foes. Reigning PGA Champion and co-leader after the second round, Rich Beem, WGC-NEC Invitational winner Craig Parry and two-time Australian Open champion Aaron Baddeley shared second at 11-under par.
Allan started strongly with a six-foot birdie putt at the first hole but failed to get anything going after that on the front nine. He parred the next seven holes before a bogey at No. 9.
The rest of the contenders inched closer to Allan but the 29-year-old Australian made a move from the pack at the start of the second nine.
Allan holed a five-foot birdie putt at the 11th hole and added a birdie at the next to get some breathing room. He fell back with a bogey at No. 13 but rebounded with a 20-footer for birdie at the 14th.
Allan lost some of his drives coming in, but at 18 he played a magnificent second shot out of a bunker and down the fairway. He knocked his third shot at the par-5 hole 20 feet short and right of the cup but lagged his birdie try three feet short. Allan ran home the par save to avoid a playoff and win the trophy.
'It's been pretty tough,' said Allan, who made nine cuts in his last 11 starts on the PGA Tour. 'I really have played well the second half of the season. I felt like my game was back to where it was when I played well out here.'
Beem never mounted a charge on Sunday with a 1-over 35 on the front side. He tallied three birdies and one bogey on the back nine but when his long eagle try at the last missed the hole, the PGA Champion shot a 69 and was resigned to a joint second place.
Parry also failed to make a move in the final round with a 2-under-par 68.
Baddeley made the biggest move on Sunday, matching Allan in first place after four birdies and a bogey through 10 holes. He dropped a shot at 11 and when Allan racked up his birdies, Baddeley dropped down. Baddeley fought back with three birdies over his last four holes for a 65.
Robert Allenby, Charles Howell III and Adam Crawford tied for sixth place at 9-under par, while Adam Scott finished alone in ninth at 8-under-par 202.
Stuart Appleby, the 2001 champion, struggled on Sunday with a 4-over 74. He finished in a tie for 30th at minus-1.
The tournament was shortened to 54 holes after Thursday's first round was wiped out due to unplayable greens.