The court today said it was passing the restraining order only in the interests of students as the admission process had already begun.
A division bench headed by Justice Abhay Oka also asked Nashik-based Fravashi International Academy to seek available legal remedy in the meantime.
The government had told the High Court that it had withdrawn the order passed by Rane.
Rane, a senior Congress leader, resigned from Maharashtra cabinet two days ago.
In his earlier capacity as Revenue Minister, he had reversed a 2006 order of the Secretary of Revenue and Forest department Avinash Hazare who had directed that the school building be pulled down and a criminal case filed against the management for running it without obtaining permission.
Nashik resident Kiran Jadhav had filed a PIL against Rane's decision. On July 7, the court had noted that prima facie it appeared that a minister cannot reverse the order of the Secretary.