The 2014 World Cup winner will return home for personal reasons, following news reports from Germany of the death of a former partner.
"This has stunned us," Flick told a virtual news conference. "Jerome came to me and asked me to return home. After a negative [COVID-19] test he will return home and not be available until further notice."
Boateng had started in their 2-0 semifinal victory over Al Ahly on Monday.
The Bundesliga champions are eyeing a sixth title in less than nine months, hoping to emulate Barcelona's six-trophy haul of 2009.
Bayern won the domestic double as well as the Champions League in 2020 along with the German and European Super Cup crowns. They are also top of the Bundesliga, seven points ahead of second-placed RB Leipzig.
Tigres stunned Palmeiras of Brazil 1-0 to become the first team from North America to reach the final.
Flick, who refused to provide any details on his possible lineup, said his team would need to be alert from the first second against the quick counter-attacking Mexican side.
"It is up to us to put pressure on our opponents and to play our game when we have possession," Flick said. "We did it well in the semi-final. I have full trust in my team."
Flick, who took charge of the club in November 2019, has had the most successful first season ever of a Bayern coach.
"We have to be alert. Tigres are very quick in their build-up," he said. "They work well down the wings and have players in the centre who score. We have to be there from the start and convert our chances this time."