The defender rejoined the Argentinian outfit in January after falling down the pecking order at United, but Rojo only managed one appearance for Estudiantes before the coronavirus pandemic saw football come to a halt across the globe.
Desabato recently admitted that he is keen for Rojo to stay in Argentina a little while longer but has now conceded that the 30-year-old will most likely return to Manchester in the summer.
"We have to wait, but Rojo is likely to leave," Desabato told Radio Late 931. "The loan is due, and if Manchester do not want to continue loaning, it's understandable."
Rojo's current deal at Man Utd is set to expire in the summer of 2021, where he has made 122 appearances across all competitions since arriving from Sporting in 2014.