The France international did the damage when shooting during a training session on Friday (AEDT) and underwent surgery soon after.
Bayern boss Hansi Flick said in a news conference that the former Lyon man will be sidelined for "at least three months".
“It’s a serious muscle injury,” the Bayern coach continued.
“When shooting (in training), he felt intense pain, there had been no warning signs.”
Reports said Tolisso cried out in pain and collapsed without any contact before being whisked away in a buggy.
He has made 22 appearances for Bayern this season and scored in Bayern's last Bundesliga match – a 3-3 draw with Arminia Bielefeld on Tuesday (AEDT).
It is the latest setback for Bayern, which also has Serge Gnabry, Douglas Costa, Leon Goretzka and Javi Martinez doubtful for next week's Round of 16 UEFA Champions League clash with Lazio.
Thomas Muller and Benjamin Pavard are also out of action after testing positive for COVID-19.
Bayern faces Eintracht Frankfurt in the Bundesliga on Sunday (AEDT).