The 24-year-old, who is currently recovering from a knee injury, has turned down an offer from the French club and will leave for South Africa at the end of the Top 14 season.
"I have signed a contract with The Sharks, which will go from June 2007 to June 2008," Michalak said.
Michalak, who has lived in Toulouse since the age of six, added: "I have wanted to leave to play in this championship for a long time, but it is difficult to leave your friends, your family and the club I've supported since I was small."
The 42-cap number 10 will not feature in this year's RBS 6 Nations Championship but could return to action with Toulouse at the end of March.
If he stays fit, he is set to be Les Bleus' first-choice fly-half at the World Cup, which is being hosted by France and begins in September.