The 25-year old defensive midfielder has been sent to Toronto in exchange for a natural second round pick in the 2015 MLS SuperDraft.
"Michael had an incredible attitude and work ethic while he was here," Sporting KC Manager Peter Vermes said.
"This decision was of mutual consent. Toronto is a team that was very interested in him and we wish him all the best with the opportunity."
Thomas joined SKC from Swedish side Ljungskile in January 2012 following a spell with Halmstads.