He was arrested and three years later found guilty of homicide, kidnapping and hiding the body of his ex-girlfriend Eliza Samudio.
The ex-Flamengo goalkeeper was released in February 2017 on parole pending an appeal after seven years in jail.
In March 2017, the 32-year-old returned to football after he was signed by Brazilian second-division side, Boa Esporte for two years.
His signing to second-division club raised Public anger, sparking protests and the withdrawal of several of the team's sponsors.
On Tuesday, Brazil's Supreme Court said in a statement that it 'has revoked its decision suspending his (Fernandes') imprisonment'.
A court source said the footballer must return to custody 'with immediate effect', AFP news agency reports.