This is a move the opposition called a constitutional coup that could extend his rule for life.
The new title for Gnassingbe, whose family has already ruled the West African nation since 1967, could raise further concerns about democratic backsliding in a region hit by a string of coups where some leaders have clung to power for decades.
He got the job on Saturday as he was the leader of the majority party, the National Assembly said in a statement.
Parliament gave politician Jean-Lucien Kwassi Savi de Tove Gnassingbe's former job as national President, a position that was downgraded and made largely ceremonial in constitutional reforms last year.
Two opposition parties; the Democratic Forces for the Republic and the National Alliance for Change, who boycott parliament called the move a "constitutional coup" in a joint statement.
"This process is neither legal nor legitimate. It is the result of an institutional hold-up orchestrated by a desperate regime, which fears more than anything the freely expressed will of the people," read the statement signed by the parties and a civil society group.
Gnassingbe's Union pour la République party and Togo's National Assembly did not immediately respond to requests for comment.
The President of the Council is responsible for co-ordinating government action, setting the broad guidelines for policy and ensuring the implementation of the decisions of the Council of Ministers, according to the Presidency's website.
The Presidency of the tiny phosphate-producing country on the West African coast had been a family affair since 1967, when Faure Gnassingbe's father, Gnassingbe Eyadema, seized power in a coup.
Faure Gnassingbe succeeded him after his death in 2005.
--Reuters--