The Brazilian winger has seven goals in his last five matches, including a brace in the 3-2 win over Los Blancos in Saudi Arabia.
Raphinha was out injured for around two months as Barca's form dipped in October and November, but has come back strongly.
"His mentality is unbelievable, his dynamic affects the whole team," Flick told reporters.
Raphinha missed a fine chance in the first half but almost immediately fired Barca into the lead in Jeddah. Then with the score tied at 2-2, the 29-year-old struck the winner from outside the area, with the help of a deflection.
"He missed the first chance but the second one, he was there and (scored) the first goal, and it gave the team more confidence," continued Flick.
"This is what Raphinha brings on the pitch, it's a lot of intensity and we need this."
Barca won the Spanish Super Cup against Real Madrid last season on their way to claiming a domestic treble.
Flick said he hoped the victory would help the La Liga leaders achieve their other ambitions this season.
"We are in a good mood, we have a lot of confidence now," said Flick, after Barca's 10th consecutive victory across all competitions.
"This final was very important for us because against Real Madrid it's always something special. Again we won a final, and this is fantastic."
Flick has won all eight finals he has competed in as a coach, including two last season against Madrid.
"When we are focused, we concentrate and play like we did today, I have a really good feeling with the team, because it's important," added Flick.
The coach brought on defender Ronald Araujo in the final stages, after the Uruguayan took a mental health break of around a month.
"To be on the pitch and to win this title means a lot for him," said Flick.
"I'm really happy that he's back, and happy that it seems like it's okay - we will support him always."