The division bench of Justices PV Hardas and Reveti Dhere allowed withdrawal, as certain amendments in the present petition were necessary because of technical errors.
Petitioner Hemant Patil, president of Rashtriya Brashtachar Virodhi Janshakti, had sought the court's direction to Maharashtra government and state's police chief to register cases against Pawar and Thackeray, whose public criticism of each other had triggered violence in February this year.
The two leaders had taken potshots at each other from public platforms, leading to clashes between NCP and MNS workers.
Pawar, nephew of NCP chief Sharad Pawar, had attacked Thackeray for mimicking political leaders in his speeches, saying it would only "entertain" but not solve problems such as the drought.
Thackeray retaliated by accusing Pawar, who handled the water resources ministry between 1999 and 2009, of being responsible for the water scarcity despite huge spending on irrigation projects.
The petitioner's lawyer said that he would file a fresh PIL, and enclose copies of FIRs lodged in connection with the instance of rioting at various places.