Zlatan Ibrahimovic rifled home the spot-kick after Xavi had gone down far too easily in the area, and the Swede's strike proved enough to give Pep Guardiola's side all three points against a limited Espanyol outfit.
Barca coach Pep Guardiola says his team battled to victory, despite fatigue.
"We have made a large sustained effort (this season) and in the second half, that showed," Guardiola said.
"They pressed and it was hard for us. We have to give this win an extra value, because it was a derby match and because the players have accumulated a lot of tiredness and debilitation in the last few weeks.
"I congratulate the players, because they have beaten a great rival and I believe this encounter is a good test for what is to come," he said, referring to Barca's forthcoming trip to Dubai for the FIFA Club World Cup.
The Catalans face Mexican side Atlante in the semi-finals on Wednesday, but must first tackle a long journey to the United Arab Emirates before that.
"We leave at 11 tomorrow and arrive at 23:30 their time.
"Spending so much time on the plane two days before the semi-finals of the World Club Championship against a rival that is already there will not benefit us," he said.