Ronaldo looked healthy to start the match, surging forward with his trademark powerful runs, but he apparently tweaked something. While he was able to leave under his own power, he wouldn't have asked to be removed from such an important game if he thought it was possible for him to run off the problem.
It's not clear exactly what Ronaldo hurt, but he was recently forced to miss time due to a left hamstring injury. That injury kept him out of the Copa del Rey final, but he was able to return for the Champions League semifinals.
The Champions League final is not until May 28, so Ronaldo should be healthy for that match if he's just experienced a bad strain or very minor tear. If he has a serious tear of a muscle, he's facing a lengthier spell on the sidelines. However, if Ronaldo has a muscle problem -- not a serious ligament issue -- he should still make Portugal's World Cup squad.