Barcelona's defence has struggled without Carles Puyol in the past, and they will be bereft of their inspirational captain for the weekend Clásico against Real Madrid after the Catalan dislocated his elbow in the Champions League win at Benfica.
The Spain international, playing his first match since recovering from a knee problem which prevented him from playing at Euro 2012, landed awkwardly after leaping for the ball at a corner.
The 34-year-old was taken off on a stretcher in the 78th minute and replaced by Alex Song as his shocked team-mates looked on.
"We are waiting for more information but he will certainly miss the Clásico," Barça coach Tito Vilanova told reporters after the match.
Puyol's defensive partner Gerard Pique is also sidelined, which may force Vilanova to start Song and one of either Javier Mascherano or Sergio Busquets against Real at the weekend.
Barca won in Lisbon, their second victory in two Group G games, thanks to goals from Alexis Sanchez and Cesc Fabregas.