The 26-year-old Australian, who has led or shared top spot after every round of the $1.3 million tournament at the Palmer Coolum Resort, fired a three-under 69 for a three-day total of 13-under par.
"I'm over the moon, I couldn't be feeling any better right now," Popovic, who won the 2012 Australasian PGA qualifying school, said.
"I knew that I had it in me and I still know that I do have one more good round tomorrow (Sunday) in me.
"I've just got to keep in routine... what I've been doing has been working this week and tonight's going to be exactly the same and so it tomorrow morning in my warm-up."
Fellow Victorian Anthony Brown scorched the course with a blistering eight-under 64 to climb up the leaderboard to second place at 11-under.
Brown, who trailed the leaders by seven shots at the start of the third round, offset nine birdies with a lone bogey on Saturday.
"I knew that there was a good round in me, I didn't really have any expectations at the start of the day but whenever you shot 64 in any tournament, let alone the PGA, you take it," Brown said. "I'm very happy with how I played today."
Australian Open champion Peter Senior (68) and Matthew Griffin (70) were tied for third at 10-under, while Brendan Jones (67) was in a pack of four players a further shot adrift.
Former US Open champion Geoff Ogilvy and China's Zhang Xin Jun, who held the share of the lead at the halfway stage, were among four more players on 8-under for the tournament.