Zlatan, who is serving a 3-match domestic ban imposed by the FA, had missed out on the club's 1-0 defeat against Chelsea in the FA Cup quarter-final last week.
But as the ban is not applicable in European matches, the Swedish striker is back in the squad.
Last week, the Red Devils had missed the services of two important players captain Wayne Rooney (injury) and Anthony Martial (illness). Marcus Rashford had started as the front striker.
Mourinho confirmed at the pre-match press conference that Rooney and Martial has still not recovered fully and thus will miss out on the match against the Russian outfit.
Addressing the media, the manager said: "He [Martial] was injured for the Chelsea match and could not be selected and if you are injured for the Monday night game, you are injured for Tuesday training session.
"If you are injured for the Tuesday training session, then it's not a case today that he could be able to play Thursday. So, he's out of my mind. I don't think about him. We have the same players we had in the last match plus Ibrahimovic."
On Rooney, Mourinho added: "Rooney is injured," he said. "He had a kick in his knee area so he stays in the medical department."
Manchester United had played out a 1-1 draw against Rostov in Russia in the first leg. They have an away goal to their advantage and will look forward to sealing a victory at Old Trafford.