The coach was left cursing his bad luck at his captain's injury, but nevertheless turned his attention to the Clasico with Real Madrid on Sunday
Due to absences at the back in the past, the Catalan outfit have been forced to convert a few players into makeshift centre-backs, with defensive midfielder Javier Mascherano being a prime example.
"We are always having problems with central defenders," exclaimed Vilanova to assembled reporters after his side's Champions League encounter. "It has forced us to convert some players in terms of position."
"Puyol has now suffered a couple of injuries this season that we might say weren't exactly normal, such as a broken cheekbone, and now a [dislocated] elbow.
"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."
The 43-year-old, who took over the Primera Division front-runners in the summer, will be overseeing his second Clasico of the season against Real Madrid on Sunday, and believes the Benfica win stands them in good stead.
"The win took a lot of effort but despite that we took three very important points here in Lisbon. We are very happy with the result.
"Alexis Sanchez is continuing to show he is a player who wants to grow. As we saw with Cesc Fabregas earlier in the season, now is the time for Alexis to push on.
"It will be a tough game against Real Madrid. What we must do now is to recover from these last two matches and start to think about the encounter at the weekend."