Tolisso, 26, tore a thigh muscle in training on Thursday.
"It's a serious muscle injury," Bayern coach Hans-Dieter Flick said.
"When shooting (in training), he felt intense pain, there had been no warning signs."
Reports said he cried out in pain and collapsed without any contact before being whisked away in a buggy.
Tolisso has made 22 appearances for the European and recently crowned world champions this season and scored in Bayern's last Bundesliga match, the 3-3 draw with Arminia Bielefeld on Monday.
It is the latest setback for Bayern who also have Serge Gnabry, Douglas Costa, Leon Goretzka and Javi Martinez doubtful for next week's round of 16 Champions League clash with Lazio.
Thomas Muller and Benjamin Pavard are also out of action after testing positive for Covid-19.
Bayern face Eintracht Frankfurt in the Bundesliga on Saturday.
