Barcelona won 2-1 in a game that was halted for 10 minutes during the second half due to crowd trouble.
Some Espanyol fans broke a fence and spilled onto the field in an attempt to escape from the flares.
Espanyol opened the scoring through Ferran (Coro) Corominas in the 20th minute, with Thierry Henry equalizing in the 77th soon after the match restarted. Lionel Messi scored Barcelona's winning goal with an injury-time penalty.
"People shouldn't be coming to the ground with flares," said Pique. "This is a show and the important thing is that people should enjoy themselves."
Barca midfielder Xavi added: "I didn't see what happened with the flares, but the important thing was that no-one was hurt."
Bojan Krkic also said: "We were aware of what happened in the stands. But after scoring the winner, the most logical thing was to celebrate with our fans."