Scott began the day with a three-shot buffer but had his lead cut to one shot after 11 holes when a thunderstorm forced a 90-minute weather delay.
But after struggling to gain any momentum before play was halted Scott made a statement with his first shot after the resumption.
The US Masters champion came within centimetres of an albatross at the par-five 12th after a majestic four iron approach from 242m before tapping in for eagle to extend to a three-shot lead at 12-under par.
He added birdies at the par-three 14th and par-five 15th to lead his playing partner Fowler by four shots.
Fowler cut the deficit to three strokes with a birdie at the 16th but there was no stopping Scott who parred the final three holes to finish at 14-under par and claim his third tournament victory of the year.
With the win Scott also becomes the sixth man to win the career Triple Crown of Australian tournaments – Australian PGA Championship, Australian Masters and Australian Open.
"This is the one I wanted," an emotional Scott said at the trophy presentation.
"It's kind of the icing on the cake for me I think this year.
"It's been an incredible year since April and I've been looking forward to coming home ever since.
"To come home and play here in front of you all has Queensland family as well who've come out here today.
"I've had a great week, I have to say this one's for my folks, especially my dad who's a PGA member, I hope he's feeling proud at the moment."
Fowler signed for a 68 to claim outright second at minus 10, two clear of Victorian trainee professional Jack Wilson who fired a 68.
Cameron Percy (68) finished a further shot back in outright fourth, one clear of Michael Wright (71).
Nathan Green (71) and New Zealander Gareth Paddison (71) were among five players at minus five in a share of sixth.
Marc Leishman (72), David McKenzie (74) and Stephen Leaney (70) shared 11th spot at four under par.
Adam Scott triumphs at Australian PGA
