The 20-year-old attacker was booked in his side's 2-0 defeat to Sevilla in the semi-final first leg, after a coming together with goalkeeper Beto, although replays showed there was no contact between the players.
Valencia's appeal over the decision was rejected by Uefa, meaning Alcacer must sit out the return at Mestalla, and Mathieu is determined to ensure that his young colleague will have one more appearance in this season's tournament - in next month's final in Turin.
"What happened to Paco is tough for everyone. We'll make even more of an effort so he can play in the final. It's a big blow for the team," Mathieu told Marca.
Valencia pulled off a stunning comeback to beat Basel in the previous round, but Mathieu has warned that his old boss Unai Emery boasts a far better side than the Swiss champions.
"Sevilla are stronger than Basel. You have to believe in us, I believe we can do it. I think we have to play an intense game, but a very intelligent one," he said.
"Sometimes you depend on the referee because, if you put your arms around them, they can earn a penalty. We've talked about this a lot in the dressing room and one of the best antidotes is to avoid silly fouls in the area.
"We'll try to make sure Unai doesn't win and that Sevilla don't reach the final. The truth is, when I played for Unai, it was inexplicable why every important game went against him. I hope there's a repeat on Thursday."