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Michalak suffered ankle ligament damage during his club's victory over Narbonne at the weekend and will be sidelined for at least two weeks.
It is a further blow to the defending European champions, who are waiting on the fitness of scrum-half Jean-Baptiste Elissalde.
The loss of the influential French international means that Toulouse coach Guy Noves may move Yann Delaigue to outside-half and Vincent Clerc may switch to scrum-half.
Clerc, capped by France on the wing, replaced Michalak at scrum-half during the match against Narbonne.
"The forwards helped me a lot and Yann was constantly giving advice and talking to me about what options to take," Clerc said.
"If required, I am ready to do it again. I am going to work hard this week so I am ready if needed."
