The Blaugrana defender has been unfortunate with his fitness in 2012, and his bad luck continued when he picked up an knock in Tuesday night's Champions League win over Benfica
The Spain international suffered the injury 76 minutes into Tuesday night's 2-0 win over Benfica, leaving a sour taste on Tito Vilanova's tongue after what should have been a morale-boosting victory ahead of Sunday's Clasico.
Real Madrid will come to Camp Nou to face a weakened Blaugrana defence, with Gerard Pique also unlikely to have recovered full fitness after picking up a foot injury in the 3-2 success at home over Spartak Moscow two weeks ago.
Puyol was grateful for Barca fans' support and wrote on his Twitter account: "I want to thank everyone. I'll soon be on top."
Earlier this year another injury forced the 34-year-old to watch from the sidelines as Spain defended their European crown in Poland and Ukraine without their skipper.