A victory in Florida in the early part of the US PGA tour three years, nine months and 16 days ago was the last time that he lifted a trophy.
His win in front of a home crowd - he has a house close by - completed a solid year and lifted him from 18th to 13th on world rankings.
The two both carded five-under-par 67s at the Royal Pines Resort on the Gold Coast, ahead of a chasing pack of five a shot further back, including New Zealander Ryan Chisnall.
Scott was the 54-hole leader by a single shot and got off to the ideal start when he birdied the first.
Cameron Davis shot a five-under 67 to move into equal third at 10-under with China's Yuan Yechun, Flanagan and Ormsby, while Andrew Dodt (68) crept into the top 10 at nine-under and 18-year-old Korean Minkyu Kim had 67 on Sunday to finish at eight-under.
Smith is bidding to become the first player to win a non-Major or WGC European Tour event three years in a row since Ernie Els won the Heineken Classic, also held in Australia, from 2002 to 2004.
Hendry led for most of the back nine but his approach to the 17th green clipped trees to leave his ball plugged in the bunker.
Scott came into the day with a narrow one-stroke lead but a birdie from close range at the first saw him double his advantage.
"After a good save on 12 it was time to do something, I was behind", said Scott after a three under par 69 gave him a 13-under winning total of 275.
"The adrenaline started pumping there the last three or four holes when I was trying to get to 10 or 11 (under-par) coming in so I could really be up there", said expectant father Flanagan.
It finishes off a nice year for me.
"It's incredibly bunched, and if it's windy tomorrow, it's going to be hard for anyone to really separate themselves unless they just play an incredible round of golf, go out there and roll in a lot of putts", said Scott.
Throughout the week Scott alluded to the need to break his winless streak in order to build towards an attempt at a second green jacket at The Masters in April, sharing the spoils of victory with his two children an added bonus.
"You want to be in contention and find out how you feel and respond and I got some of that today and if I happen to be in that position Sunday at the Masters I can draw on it".
Michael Hendry battled sore ribs and finished his tournament with successive bogeys.