Franjic underwent scans on his right hamstring on Saturday and they confirmed he has torn the muscle, which will rule the right-back out of the rest of the tournament.
Australia coach Ange Postecoglou labelled the injury a 'massive disappointment' - both for Franjic but also for the team after the right-back's strong first half in Cuiaba.
"Ivan's no good, he had a scan today and has a fairly significant hamstring tear. That rules him out for the tournament, and that's a real disappointment," Postecoglou said on Saturday.
"He was growing into the tournament and into the game; the first 15 minutes everything was a bit quick for him but after that he settled into the task and set up the goal really well.
"He was getting to grips with it so it's a massive disappointment. I'll talk to him later but there's not a lot you can say. But what's tasted should be motivation to come back for more."
The Brisbane Roar defender had created Australia's goal in the 3-1 loss to Chile, crossing for Tim Cahill to score.
McGowan is better known as a central defender and was ripped apart at right-back in Australia's 6-0 loss to Brazil in September but insisted he will be comfortable as a full-back.
"I played a lot of right-back when I was at Hearts, I don't feel out of place there at all," McGowan said.
While Postecoglou agreed McGowan may start in Australia's next match against the Netherlands, the 48-year-old coach also hinted he may try something different.
"Ryan is a solution, there could be a couple of different things in the way we approach things," Postecoglou said.
"Holland represents a different problem to Chile, so we'll have a look in the next couple of days."
