A Bench comprising justices G S Singhvi and Kurian Joseph stayed the notifications issued in this regard on February 9 and March 14.
The bench said the senior most Dean of each university will perform the function of VCs.
The bench passed the order on the petition filed by the Bihar Government and some of the professors who have challenged the appointment made by Konwar.
It posted the matter for further hearing on April 14.
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The High Court had also directed the Chancellor to make a fresh list of candidates for appointment of the VCs and Pro-VCs within 30 days.
However, same persons were later re-appointed.
Shambhu Nath Singh and Arun Kumar were appointed as the vice-chancellor of Patna University and Magadh University respectively.
Md Samsuzoha was appointed at the Mazhrul Haque Arabic and Persian University VC and Ram Vinod Sinha was made the vice-chancellor of B N Mandal University, Madhepura.
Arvind Pandey and Shiv Shankar Singh were made the VCs of Kameshwar Singh Sanskrit University, Darbhanga and Veer Kunwar Singh University, Ara respectively.
After the announcement that Konwar was being replaced as Bihar Governor, he appointed Anjani Kumar Sinha as VC of Tilka Manjhi Bhagalpur university and Raja Ram and Padmasha Jha as pro-VC of Patna University and Bihar University, Muzaffarpur respectively on March 14.