The Toulouse number 10 was ruled out of the visit of Italy to the Stade de France with neck and shoulder injuries.
Michalak picked up the injury during France's 35-17 win over Ireland in their tournament opener.
"I was pinned to the ground by (centre Kevin) Maggs in the middle of the second half and I stayed on the ground for a while," Michalak explained.
"The pain remained until the end of the match.
"I was worried because I knew that it was not a benign pain and the medical examinations I underwent on Monday confirmed that feeling.
"This is wise not to play against Italy. I have to rest for two weeks but I will be ready for the away match against Wales in Cardiff.
"The injury is not serious, I can run and kick but it's better not to take any risk."
Coach Bernard Laporte and team manager Jo Maso explained they have rested Michalak to avoid being ruled out for the rest of the competition.
"We could have given him painkilling injections," Laporte said.
"But it would not have been fair neither for Michalak nor for his club.
"The match against Italy is not a final, that is why we can afford to rest him now. There is no need to take any risk."
Michalak, who has returned to Toulouse, will be replaced at fly-half by debutant Julien Peyrelongue.
Scrum-half Jean-Baptiste Elissalde will be the goalkicker against Italy.
"I am used to the kicking role," added Elissalde, who will start an international clash for the second time in his short career.
"But I hope we won't need it too much to beat Italy. Even if Julien is not quite as quick as Fred, I think he has all the qualities to adapt fast to the French team's game, the same way I did last week."