Cubarsi had ten stitches in his face after suffering a horror facial injury during Barcelona's 5-2 win over Red Star Belgrade in the Champions League on Wednesday night.
At the stage, it appeared to be highly unlikely that the Spaniard would be involved against Real Sociedad this weekend, while he has been left out of the Spain squad for their upcoming matches in the UEFA Nations League.
La Roja head coach Luis de la Fuente said that Cubarsi needed time to recover from his injury, telling reporters at his press conference: "He had a significant wound, with nine stitches and very deep. We always take care of our players. Pau has to have a few days until the wound heals. We must not take any risks."
However, Cubarsi trained in a mask on Saturday, and Flick is confident that the 17-year-old will be able to take to the field for the La Liga clash with Real Sociedad on Saturday night.
Cubarsi trained in a mask ahead of Real Sociedad clash
"I think Pau will be there, he trained with us throughout the session," said the Barcelona head coach.
Cubarsi has been a vital player for Barcelona this season, making 16 appearances in all competitions, and he has formed a strong partnership with Inigo Martinez in the middle of the defence, with Ronald Araujo yet to play this term due to injury.
Dani Olmo had emerged as a late doubt for the clash with Real Sociedad due to illness, but Flick is also confident that the Spain international will be available for the trip to the Basque outfit.
"Dani Olmo felt a little bad, and uncomfortable during the night. This morning he was a little better, they are treating him and we'll see although I think he will be ready tomorrow," added the German.
Barcelona have won their last seven games in all competitions
Barcelona will enter Sunday's clash having won their last seven matches in all competitions, including their last four in La Liga, and they currently sit nine points clear of second-placed Real Madrid at the top of the La Liga table.
"We want to win every game. Now we play against Real Sociedad and I really like the way they play. They are a technical and very intelligent team. It will be an interesting game tomorrow," Flick told reporters.
"There are many things I'm proud of. I always look at the last game and against Red Star we saw that we finished together."
Barcelona are yet to name their squad for the clash with Real Sociedad, but Araujo, Andreas Christensen, Marc-Andre ter Stegen, Marc Bernal, Eric Garcia and Ferran Torres will all miss out on Sunday due to injury problems.