As soon as Sai's counsel got up to start advancing arguments, Justice U U Lalit, who was sitting with senior judge Justice M B Lokur on the bench, wished to recuse himself from the hearing.
The court then referred the matter to Chief Justice J S Khehar for it to be listed before another bench.
Earlier, the Gujarat High Court had rejected the bail application of Narayan Sai, 44, who is at present lodged in Surat jail.
Sai was arrested for repeatedly sexually assaulting one of the two Surat-based sisters, who was the inmate of his ashram here between 2002 and 2005.
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In February, 2014, the Surat police had filed a charge sheet in a special court against Sai and eight others under various sections of the Prevention of Corruption Act in connection with the bribery case.
The police had named nine persons, including Sai, as accused in the charge sheet.
The sisters had lodged two different complaints against Sai and another against his father accusing them of rape, sexual assault, illegal confinement and other charges.
The police had booked Sai under the various IPC sections including rape, unnatural sex, molestation, wrongful confinement, unlawful assembly, rioting armed with deadly weapon, criminal intimidation and criminal conspiracy.
In her complaint, the younger of the two had accused Sai of repeated sexual assault between 2002 and 2005 when she was living at the Surat ashram.