Bruno Fornaroli opened the scoring in the 16th minute, then headed home his 17th goal of the season in the 53rd to draw two clear of Perth marksman Adam Taggart in the golden boot race.
Perth hit back through Daniel Bennie in the 61st minute and were denied a handball penalty 12 minutes later at AAMI Park on Sunday.
Daniel Bennie's goal wasn't enough to save Perth from defeat. (Steven Markham/AAP PHOTOS)
Third-placed Victory are on 38 points, two shy of second-placed Central Coast, who have a game in hand, while 10th-placed Perth are 10 points outside the top six.
"Happy overall with the performance and we got the result we deserve," Popovic said.
"It was a little tight, obviously with them scoring the goal, but I thought we saw out the game very well."
Daniel Arzani notched an assist, seven chances created and six successful dribbles, along with winning 10 duels as he played just over 90 minutes.
"Very good, his most complete game in terms of his periods of not being involved are getting less," Popovic said.
Victory's Daniel Arzani notched an assist, seven chances created and six successful dribbles. (Morgan Hancock/AAP PHOTOS)
"What we want is the all-round game. In the 90th minute when he runs back and makes a tackle on the edge of the box and wins the foul, that's football. That's how the game needs to be played, and he's getting better.
"We love having him here and we've got to keep pushing him to fulfil the talent that he has."
For the opening goal, Arzani cleverly back-heeled Damien Da Silva's long ball to the top of the box.
Zinedine Machach took a touch and prodded it to Fornaroli.
The striker spun on the ball and fired past Oli Sail, with the help of a slight deflection.
For Victory's second, Machach found Arzani on the edge of the area and the winger delivered a wonderful ball to the back post for Fornaroli to glance home.
Perth then caught Victory on the counter, with Jarrod Carluccio beating Da Silva and cutting back for an unmarked Bennie to prod home his first league goal.
Victory's Roly Bonevacia gave away a handball free kick just outside the box in the 73rd minute.
After a VAR review, referee Ben Abraham ruled the incident had happened inside the box, but wasn't a handball.
"At the time I was disappointed that the foul was given because it was never an intentional handball and his hand was against his body," Popovic said.
"I'm actually glad they reviewed it because it took away the free kick."
Perth coach Alen Stajcic said: "I couldn't tell. I thought they were checking it to see whether it was in or out because the original decision was handball from what I was told.
"... And then it apparently wasn't handball, so it's irrelevant. That was their call, that it wasn't handball at all."
As they have done all season, Perth kept Victory on their toes until the closing seconds but couldn't find an equaliser.
"They were the better team on the day, but there wasn't much in it," Stajcic said.
Victory face Melbourne City next Saturday, and Perth have a tight turnaround to play Sydney FC at home on Wednesday, before hosting Adelaide on Sunday.
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