Germany's latest wonderkid suffered the injury in Bayer Leverkusen's 1-0 home loss to FC Cologne in the Bundesliga on Sunday.
Initial prognosis have revealed that Wirtz will be out for several months putting him in danger of missing out on the 2022 FIFA World Cup in Qatar later this year.
"Bayer 04 Leverkusen will have to do without midfielder Florian Wirtz in the long term," a statement on the club's website read.
"The 18-year-old national team player tore the anterior cruciate ligament in his left knee in the Bundesliga game on Sunday afternoon, March 13, against 1. FC Köln (0-1).
"This is the diagnosis from an immediate MRI scan. The Werkself will therefore be without Wirtz for several months."
The 18-year-old has won four caps for the Die Mannschaft.
Flick had big plans for Wirtz in Qatar later this year and he has rued the prospect of having to do without the talented youngster.
"He is one of the greatest talents that German football has produced in recent years," Flick told the DFB's official website.
"That's why we were all shocked when we found out about his cruciate ligament rupture. I've already phoned him and tried to encourage him.
"He's still young, he'll come back at least as strong, I'm sure of it. He gets our full support.
"We wish him all the best and keep our fingers crossed that the healing process goes as optimally as possible."
Wirtz has made 31 appearances for Bayer Leverkusen in all competitions this season, recording 10 goals and 14 assists.
