The central defender returned from a knee injury suffered in January to feature in Saturday's league clash with Madrid at the Bernabeu.
However, he had to be carried off on a stretcher with a hamstring problem after 58 minutes and had the muscle heavily strapped up in the dug-out.
With the bitter rivals clashing again in Valencia on Wednesday - the second of four meetings this month - Puyol admits his participation in the final remains up in the air.
"I'll definitely be there," the skipper told fcbarcelona.cat. "But playing or not, I don't know."
Puyol was delighted to return in such an important game, when a 1-1 draw effectively wrapped up La Liga as Pep Guardiola's side maintained their eight-point lead.
"I felt very good on Saturday, with loads of enthusiasm and excitement," he said. "It's been three hard months that were very tough for me.
"It was the perfect place to make my comeback. In the first half I felt really good until I started having some problems."
