The Brazil forward deserved being singled out for extra praise from Barcelona's coach. He had just led a thrilling 4-3 fightback over Celta Vigo by scoring two late goals including a clutch penalty for an injury-time winner.
Barcelona remained on pace for the Spanish league title as they opened up a seven-point gap over Real Madrid on Saturday before the defending champions host Athletic Bilbao on Sunday.
"It was amazing to see at this stage how this team gives everything to never give up," Flick said. He added that at halftime he told Raphinha he needed him "as a leader" on the field.
Raphinha's double let him reach 30 goals in all competitions this season, the best of his career.
The loss might come at a price, however.
Barcelona top scorer Robert Lewandowski asked to be substituted in the final minutes while touching his left thigh.
"We have to wait until tomorrow," Flick said.
There is no let up for Barcelona with three titles in play.
Barcelona face Mallorca in the league on Tuesday and Real Madrid in the Copa del Rey final next weekend. Four days after that they will start their Champions League semi-final against Inter Milan.
It looked like another easy win for Barcelona when Ferran Torres fired the hosts ahead early.
But Celta striker Borja Iglesias started his spectacular three-goal performance just three minutes later, scoring on the break after Barcelona goalkeeper Wojciech Szczesny failed to reach a low cross.
Iglesias stunned the home fans again by scoring twice more in the 59th and 62nd from passes from Celta's own area that were poorly defended by Barcelona.
Iglesias got his second goal after Frenkie De Jong let a long goal kick that looked harmless bounce past him, apparently thinking a teammate would control it. Instead, Iglesias pounced on the ball and drilled a shot inside the far post.
He made it a hat-trick when Barcelona's defence let him run onto a long ball and dink his shot past Szczesny.
Barcelona looked done but Flick's side quickly rallied behind Raphinha — with some help from substitutes Olmo and Lamine Yamal.
Raphinha slipped a ball through for Olmo to take Barcelona's second goal. He then rose up to thump in Yamal's cross with a powerful header.
And with Lewandowski on the bench, Raphinha beat goalkeeper Vincente Guaita from the high-pressure penalty deep in injury time after a video review convinced the referee to penalise a foul by Celta defender Yoel Lago on Olmo.
Celta, who held Barcelona to 2-2 in their other meeting this season, fell into eighth place.
Third-placed Atletico Madrid's visit to Las Palmas was also decided deep in stoppage time, when the hosts got a goal from Javi Muñoz to snatch a 1-0 upset
The loss in the Canary Islands left Atletico 10 points adrift of Barcelona with six rounds remaining.
Las Palmas escaped the relegation zone after Muñoz poked a ball past Jan Olbak that Atletico failed to clear.
Mallorca moved into seventh after a 0-0 draw with Leganes, while Umar Sadiq struck to help Valencia rally for 1-1 at Rayo Vallecano.
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