The 26-year-old Australian, who led or shared top spot after every round of the $1.3 million tournament at the Palmer Coolum Resort, began the final day two shots clear and carded a final-round three-under 69 for a 16-under par 272 total.
The victory was made even more emotional for the Victorian after his father was diagnosed with bone cancer earlier this year.
"He's the reason (I won) because of what he's going through," Popovic said. "I'll come home after a bad round and say to him 'golf is a hard game' and he'd say 'look what I'm going through'.
"It puts things into perspective."
Popovic nearly quit golf to look after his father but decided to play on at his insistence.
"When I stood over some putts and had some doubts, I thought of his words. They got me back on track," he said. "My dad is why I am more confident and back myself and push so hard on the golf course.
"I can't wait to give him a big bear hug."
Popovic, ranked 1,251st in the world, said his outlook towards golf has changed.
"Two weeks ago I entered Q-School (qualifying school) for next year for Australia and was thinking I would just play one tour because of my father's illness, but now next year is just going to be bigger and better and hopefully he keeps pushing on as well," he added.
"My goal with golf is to win a major championship. I don't feel it's that far off.
"I'm going to walk away thinking if I keep doing this, I'm going to get there."
Fellow Australians Anthony Brown and Rod Pampling, who saw his title chances vanish with a stunning late collapse, finished tied for second on 12-under.
Popovic, who won the 2012 Australasian PGA qualifying school, started brightly with three birdies in his first five holes but a double-bogey on the eighth saw him fall behind a surging Pampling.
The 43-year-old began his final round with six consecutive birdies and took the outright lead by the turn but bogeys on the 16th and 17th and a double-bogey on the last hole allowed Popovic to cruise to victory.
"I knew I had to make a birdie on the last to put some pressure on him, I was trying to win it," Pampling said of his approach shot to the last green which landed in the water.
Former US Open champion Geoff Ogilvy and Brad Kennedy finished on 11-under for the share of the fourth spot.