Justice Girish Gupta set aside the order of Justice Dipankar Dutta who had directed filing of an FIR against Pal.
Justice T Chakrabarty, the brother judge, however, dismissed appeals of both the West Bengal government and Tapas Pal.
The matter will now go to a third judge to be nominated by the Chief justice.
The interim stay on Justice Dutta's order would however continue for three weeks, the division bench directed.
On August 1, after completing the hearing, the High Court had said it would give its verdict on August 13 and extended the stay on registration of FIR against Pal for his 'shoot and rape' comments.
It had extended the stay till August 14 on the execution of a single bench order directing registration of an FIR and CID probe against Pal for his objectionable comments against women.
Justice Dipankar Dutta had earlier ordered registration of FIR and transfer of the case to CID within 72 hours.