Puyol facing six weeks out with knee injury
The 34-year-old tried to play on after having some treatment on the touchline following the incident, but lasted only a few more minutes before giving way to Javier Mascherano in the 57th.
"Puyol is very important for us and we hope he recovers soon," Barca coach Tito Vilanova told a post-match news conference. "We always seem to have problems with injuries to the central defenders."
Puyol had just returned to action after fracturing a cheekbone against Osasuna last month and had surgery on his right knee back in May which forced him to miss Spain's triumphant Euro 2012 campaign.
If tests on Sunday confirm the initial assessment, Puyol will miss Barcelona's opening Champions League game at home to Spartak Moscow on Wednesday and the visit of Spanish champions Real Madrid in the league on October 7.