With his team trailing 2-0 in their semi-final encounter, Cherki came off the bench in the 73rd minute in place of defender Fernando Marcal as the Ligue 1 side chased the game.
Unfortunately for Lyon, their Champions League run came to a close as two first-half goals from Serge Gnabry and a late strike from Robert Lewandowski gave the Germans a comfortable 3-0 win.
Bayern will move on to face PSG in the final on Sunday at Estadio da Luz in Lisbon.
It was still a history-making cameo for Cherki, who only turned 17 on Monday. The teenager is only the fourth 17-year-old to appear in a Champions League semi-final after Bojan, David Alaba and Julian Draxler.
Previously, the youngest player to appear in a Champions League knockout-round match was Kenneth Zohore, who set the mark for FC Copenhagen in February 2011.
Cherki has announced himself as one of world football’s top prospects in the 2019-20 season, having already made 12 senior appearances and scored three goals for Lyon’s senior team prior to Wednesday.
In June, Lyon president Jean-Michel Aulas revealed that Manchester United and Real Madrid were both interested in signing Cherki before he committed to a professional contract with Lyon.
“He’s undoubtedly a player who will go to the highest level,” Aulas told Telefoot. “That’s why we did everything we could to sign him.
“We want him to succeed with Lyon. We want to support him and that’s why we’re trying to move his career on. In years to come, we want him to become not only a leader for our attack, but a leader from the academy.”
His performances even drew praise from Kylian Mbappe, who tweeted: “Don’t speak too much about age.”