Felipe Melo was injured by a tackle by Portugal's Pepe as the two players feuded for most of the first half, both receiving yellow cards for tackles on each other, and was substituted just before halftime.
"It's the left ankle, it's a worry because it was a bad knock," Runco told reporters.
"At the moment, it's difficult for him to even walk. The problem is the time for recovery, 48 hours is a very short period to get over this. We'll have to wait and see what happens."
Felipe Melo, who admitted recently that some of his tackles are over the top, has been a key player for Brazil in the last year.
Forward Robinho, rested after he complained of muscular pains, said he would be ready for Monday's game against the second-placed team in Group H at Ellis Park.
"It's just a bit of discomfort, so it was fine for the boss to leave me out as a precaution as we were already qualified," he told reporters.
"If it had been a decisive game, I would have been available. For Monday, there's no problem, I'm ready to play.
