Judicial Magistrate C T Gote accepted the application of the Law and Judiciary department, filed through district government pleader Ujjwala Pawar.
The Sena, then in opposition, had called for a shutdown on December 28, 2010 to protest removal of a statue of Dadoji Konddev, a historical figure associated with King Shivaji, from the Lal Mahal palace in Pune.
Sena activists torched 13 buses and disrupted traffic on the Mumbai-Pune highway. Some activists were detained in Lonavala for stopping two trains.
In 2015, the state government had sought permission from the court to withdraw the case, however, the court had then rejected the plea.
Today, accepting the application, the court stated in its order, "The consent is granted to withdraw from the prosecution."
Detailed order is not available yet.