Having already qualified for next year's World Cup in North America, the Socceroos are ramping up their preparation with friendlies against hosts Canada and the United States.
Watford star Irankunda netted in the 71st minute, and goalkeeper Paul Izzo, starting ahead of captain Maty Ryan, was magnificent in Australia's seventh straight win.
After Irankunda and Mohamed Toure starred against New Zealand, the close friends vindicated Popovic's decision to start them at Montreal's Stade Saputo.
Australia scored when Connor Metcalfe released Toure on the right and the striker cut the ball back into a dangerous area.
As Canada defender Nico Sigur dithered in taking possession, Irankunda slid in from the blind side to score his third international goal.
Tempers flared late and Popovic substituted Irankunda just after the youngster got a yellow card amid an injury-time scuffle, but embraced the 19-year-old in a bear hug as he came off.
"That's something more for me and him that we shared," Popovic said of their discussion.
"I'm just proud of his contribution. He's a young man that has so much growth to come. Now in the last two games, he's scored goals for Australia.
"He's 19 years old and we have a striker (Toure) that's 21 starting here, away from home against Canada, so very proud of them.
"And that's part of football. He doesn't back down. He was coming off regardless of what happened there.
"But yeah, the boys did well and happy for the two young boys up front, contributing with the goal, but overall a very strong performance."
After surviving a dour first half on Friday (local time) dominated by Canada, the Socceroos came to life with the introduction of second-half substitutes Jordy Bos, Lewis Miller and Patrick Yazbek.
Izzo made eight saves, including a world-class effort with his leg to deny Jacob Shaffelburg in the 90th minute,
"He's stepping up," Popovic said of Izzo.
The Socceroos are now unbeaten in their 11 matches under Popovic.
In just the third minute, Tajon Buchanan burst into the box, but the excellent Alessandro Circati, again given the captain's armband on his 22nd birthday, slid in with a perfectly timed tackle to clear it to safety.
Throughout the first half, the Socceroos struggled to get on the ball or to keep possession, and Buchanan caused makeshift left wing-back Kye Rowles plenty of issues down the right flank.
But otherwise world No.26 Canada struggled to break down the Socceroos' organised defence, or Izzo.
Australia had just one shot to Canada's seven at the break but came out of halftime with more energy and impetus, and the introduction of Bos, Yazbek and Miller in the 57th minute delivered immediate energy.
Toure and Circati both missed chances close to the hour mark, then the ball pinballed around the Socceroos' defensive area in the 70th minute before they cleared it to safety.
The Socceroos couldn't find a second goal, and Izzo came to their rescue in a spiteful final few minutes.
Popovic welcomed the opportunity to head to Denver, Colorado, to face the world No.16, the United States, at Dick's Sporting Goods Park on Wednesday (AEDT).
"There's another challenge for us, with the altitude, so that's something we want to experience, and we'll see how we handle that on (Wednesday)," he said.
"But it's a good test for logistics, a good test for the conditions, and obviously when you look at the opponent, it's a major test in terms of who we're playing."
