Rubabuddin had sought withdrawal of the petition on grounds of ill health.
Last month, the high court had given him time to rethink his decision.
Justice A V Nirgude today again asked Rubabuddin if he still wanted to withdraw the petition, to which he replied in the affirmative.
The court accepted his statement and permitted withdrawal of the petition and disposed it of.
On December 30, 2014, a CBI court in Mumbai had discharged Shah in the alleged fake encounter cases saying there existed "no case" against him and that he had been implicated for "political reasons".
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