The striker won the penalty when he was tugged back in the box by Alejandro Catena, who was sent off.
The champions took the lead through Jules Kounde’s header in the first half but Chimy Avila drilled the hosts level with less than 15 minutes remaining.
Xavi brought on new loan signings Joao Cancelo and Joao Felix in the second half as Barcelona, third, stayed on league leaders Real Madrid’s tail, two points behind their arch-rivals after four games.
The coach started 16-year-old Lamine Yamal on the right wing again after his impressive display last weekend and his first call-up to the Spanish national team on Friday.
However, it was veteran forward Lewandowski’s penalty which was crucial for Barcelona this time.
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