It also restrained him from attending the ongoing Winter Session of Parliament. The session is scheduled to end on Friday.
"The order (of the Rajya Sabha chairman) cannot be stayed at this stage," Justice Vibhu Bakhru said and made it clear that the interim directions would be in force till the disposal of Anwar's main petition.
The judge directed that in the interim period, all prerequisites and privileges associated with membership of the House shall continue.
It asked the the Upper House chairman and Singh to file their counter affidavits and fixed the main petition for hearing on March 1 this year.
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On December 15 last year, the high court had granted similar interim relief to Sharad Yadav on his plea challenging his disqualification.
The interim order had come on Yadav's plea challenging his disqualification on several grounds, including that he was not given any chance to present his viewpoint by the Rajya Sabha chairman before passing the order against him and his colleague on December 4 last year.
Anwar, who had rebelled against the official JD(U) faction led by Bihar Chief Minister Nitish Kumar after the latter joined hands with the BJP, has termed the Upper House chairman's order as "perverse, contrary to the rules of natural justice and tainted with malafide".
The plea has stated that the filing of an application before the Election Commission of India (ECI) by the Yadav-led faction for recognition as the real JD(U) could not lead to the inference that he voluntarily gave up his membership of the party.
Naidu, while disqualifying the two, had accepted the JD(U)'s contention that they had "voluntarily given up" their party membership by defying its directives and attending events of opposition parties.
The JD(U) had sought their disqualification on the grounds that they had attended a rally of opposition parties in Patna in violation of its directive.