Commodore Puneet Kumar Bahl handed over the charge to Captain Pisharody at the base premises, an official release said.
Bahl, who has been promoted as Rear Admiral, would be moving to Headquarters, Integrated Defence Staff (IDS) at New Delhi, it said.
Indian Navy's long range maritime reconnaissance aircraft such as Tu-142 and P8I are among the aircraft fleets based in INS Rajali.