Lewandowski has missed the last two matches with hamstring discomfort. Pedri, who has also has a hamstring problem, was absent for the midweek win over Guadalajara in the Copa del Rey last 32.
"Pedri is not available for tomorrow’s match. I’m not happy about it, but it’s part of football. Hopefully, he’ll be able to be with us again in the next game," Flick told reporters on Saturday.
"(Lewandowski) is an option for tomorrow. He can play. We didn’t want to take any risks and now he’s available."
The trip to third-placed Villarreal is Barca's last match before the Christmas break, and Flick said he was looking to end the calendar year with a seven-match winning streak.
"It's been an impressive year, full of success," said Flick, who guided Barcelona to victory in LaLiga, the Copa del Rey and the Spanish Super Cup this year.
"I’m very happy to have experienced all of this in Barcelona. But that’s part of the past; now we have to keep working, because we have big objectives for this season."
