The Argentine has been out of action since April after rupturing his anterior cruciate ligament in the Europa League quarter-final win over Anderlecht.
Rojo trained alongside his teammates on Tuesday ahead of United's Champions League tie at Benfica on Wednesday night, but Mourinho admitted that the 27-year-old needs a little longer to recover fully.
"Rojo is not coming to play but he is coming with the team to train today with the group," Mourinho told MUTV.
"Tomorrow, individually, but he's coming [back]. I would say, probably in two weeks, Marcos is ready to play."
Rojo has made 95 appearances for United since his 2014 move from Sporting Lisbon.