Bos suffered the injury when he was clattered in a challenge late in the first half of Australia's round-of-32 loss to Egypt.
The wing-back was prone on the turf for several minutes, not moving his left leg, then had to be helped from the field by trainers and was forced out of the game.
Bos later returned to the bench on crutches and with his left knee in a brace.
The 23-year-old went for scans on Saturday (Sunday AEST) - where he will hope he has avoided an ACL injury or anything similarly serious.
While Aziz Behich was strong and Kai Trewin worked hard when he came on in Bos's stead, there is no replacing the dynamic 23-year-old.
"He's struggling, so it was a big loss for us," coach Tony Popovic said.
"He had to come off, not a very good challenge. Unfortunately, it wasn't even a yellow card."
The timing couldn't be much worse for Feyenoord dynamo Bos, who has overcome a run of serious hamstring injuries to establish himself as one of Australia's best players.
The defender has shone for the Dutch Eredivisie outfit and had been widely tipped to secure a move to a Premier League or Bundesliga club, especially after his devastating performance against Paraguay.
The severity of Bos's injury could well affect whether a club pursues him in the coming weeks.
"Obviously he's unbelievably disappointed," veteran midfielder Jackson Irvine said.
"I didn't really get a close enough look at what's happened, obviously it's not great seeing him in a knee brace, but we're just hoping for the best for him.Â
"Against Paraguay was one of the best individual displays I've seen from from a Socceroo at this level.
"He's an incredible player, and he'll be a huge part of this team and the future of it."
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