According to LiveScore, the 23-year-old Borussia Dortmund left-back was replaced on 66 minutes following a heavy tackle and is now expected to miss the remainder of the tournament and the start of next season.
But, Portugal boss Fernando Santos said "Raphael went to hospital. We think he might have fractured his leg, unfortunately".
"That was a bad moment for Portugal. He is a fantastic boy and he played very well.
"He is a top quality player and this might have an impact on the beginning of his new season as well.
"We are sad about that, but let's see what the exam results tell us. I hope they are not as serious as we believe they are at the moment, I hope not."
Guerreiro set up Cristiano Ronaldo for Portugal's only goal in the game on eight minutes.