Messi set to miss Inter showdown
Messi was replaced in the 75th minute by Bojan Krkic at San Mames with what appeared to be a torn left thigh muscle, the club said.
"We took him off because he was in pain. We'll do more tests tomorrow but the outlook is not good," Guardiola told a news conference.
Sweden striker Zlatan Ibrahimovic also missed the game with a thigh strain, while Eric Abidal and Yaya Toure were laid low with the HIN1 virus and Rafael Marquez also missed the trip to Bilbao with suspected swine flu.
The mounting injury list comes at a bad time for the European champions who host Inter Milan in the Champions League on Tuesday when a defeat combined with a win for Rubin Kazan would put them out of the competition.
Next Sunday they take on the new La Liga leaders Real Madrid at the Nou Camp.