The incident had occurred in Pimpri city on Saturday in apparent protest against minister Patil's controversial remark about Dr BR Ambedkar and social reformer Mahatma Jyotiba Phule.
Jayant Naiknavare, deputy inspector general of police (VIP security), will replace Pandey as the Nashik police commissioner.
Heavy police security was deployed in Mumbai in the wake of Thackeray's call for "silencing" loudspeakers atop mosques.
One person was killed and three others were injured in a fire that broke out in a container yard near Jawaharlal Nehru Port Trust at Uran in Navi Mumbai on Wednesday, resulting in an explosion, police said.
Heavy police security had been deployed at various places following the large scale protests.
The 16-year-old boy allegedly raped the girl at an isolated place at Talegaon village under Trimbakeshwar taluka in the district on Saturday, Trimbakeshwar police station in-charge Mukund Deshmukh said.