The Spanish centre-back dislocated his elbow after landing awkwardly on his arm in the latter stages of the second half at Estadio da Luz, and was immediately substituted.
"Carles Puyol has now suffered a couple of injuries this season that we might say weren't exactly normal, a broken cheekbone and now a [dislocated] elbow," said Vilanova.
"We'll have to wait and see how long he's going to be out for but he'll be an important loss for us.
"We are always having problems with central defenders. It has forced us to convert some players in terms of position."
Puyol had only recently recovered from a knee ligament injury.