A bogey on the last dropped him to 20 under for the tournament but the West Australian's fourth career win was all but sealed earlier on Sunday by a brilliant chip-in from 50 metres for eagle on the ninth.
That put four shots between him and nearest rival Rikuya Hoshino (67, 68, 64, 68) at the turn.
A bogey on the 10th was a rare blip, Lee (64, 66, 66, 68) again chipping within a metre of the 12th to reinstate the buffer and cap a dominant week at Brisbane's Royal Queensland.
There were no signs of nerves after he got up-and-down for par on the 17th.
Lee donned a chef's hat in a nod to his 'Let Him Cook' motto, leading a clap with the crowd then running to the 18th tee to drill his tee shot down the middle of the fairway.
He found a greenside bunker and missed the putt to drop a shot and finish two short of the tournament record, 22 under set by Jed Morgan early last year.
Marc Leishman carded a seven-under 64 on Sunday to surge into third ahead of Curtis Luck (15 under).
Adam Scott (12 under) stood still after he'd cruised into title contention at the tournament's midway point to finish sixth and continue his near four-year title drought.
Defending champion Cameron Smith crashed out after two forgettable rounds and spent the weekend working on his putting over the weekend ahead of the Australian Open, which begins in Sydney on Thursday.
🚨 AN ACE FOR — PGA of Australia (@PGAofAustralia) @joaconiemann 🚨#AusPGA | #visitbrisbane pic.twitter.com/CJ5yKkBOrqNovember 26, 2023
Chile's Joaquin Niemann (13 under) landed an ace on the fourth hole just after Hoshino had erased Lee's overnight lead of three shots in a manic opening 30 minutes of play.
But Lee steadied, almost holing an ace of his own on that same hole to quickly reinstate some breathing space.
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