The Uruguayan, 25, was signed from Nacional two years ago but made just six league appearances for Boro, three of them as a substitute.
He ended last season on loan at Spanish second-tier side Real Oviedo, where he played seven times and scored once.
Boro say they have decided to end his contract in order to help him find a new club.
Winger Carlos de Pena has left Middlesbrough after his contract was terminated by mutual consent.