Garcia was instrumental in Barcelona's 2-0 victory, producing a series of outstanding saves, with the league leaders extending their lead at the top of the LaLiga standings to 49 points.
"The first thing I have to do is thank Joan Garcia," Flick told reporters. "He is one of the best goalkeepers in the world. We suffered, but we took the three points and that is the message we send to LaLiga."
Flick praised the goalkeeper's composure, particularly given the hostile reception he faced on his return to the RCDE Stadium, where he had previously come through the ranks.
"Fantastic," the German manager said when asked about Garcia's mental strength. "I think he will not forget what he lived here, because he played for Espanyol and they gave him his opportunity. Now he plays for us, and he was one of the reasons for the win."
Garcia was jeered from the warm-up, with banners aimed at him displayed in the stands, including images of rats and mock banknotes bearing his face. Flick said the 24-year-old appeared unaffected before kickoff.
"Of course I spoke with him," Flick said. "I saw him calm, as always. Focused, convinced. The great teams have the best goalkeepers, and he is one of them."
Espanyol coach Manolo Gonzalez, whose side created several clear chances but failed to score, declined to discuss Garcia's performance.
"I'm not going to talk about Joan," he said. "Whatever I say will be twisted. I don't want to go into that.
"We were very close to winning and it slipped away... today we should have won."
Turning his attention to the Super Cup, Flick added that the victory would give his side a morale boost ahead of Wednesday's clash with Athletic Bilbao.
"It's not easy after the Christmas break to play this match and go straight into the Super Cup," the German said. "But this victory will give us confidence."