Raj, along with other MNS activists, had been booked under sections 336 (act endangering life or personal safety of others) and 427 (mischief causing damage to the amount of fifty rupees), after a mob damaged two state transport buses at Mazalgaon on October 21, 2008.
Initially, two cases were registered against the MNS president and his supporters by drivers Shaikh Khwaja Shaikh Unus and Uttam Saundarmal respectively but were later clubbed into one.
Thackeray was shown as an absconding accused in the chargesheet filed against him in the court of Judicial Magistrate First Class Aparna Navandar in 2009.
The court had recently issued an arrest warrant against him for his failure to appear before the court.
"We have got the warrant cancelled and secured bail for Raj Thackeray," defence counsel V B Lavate said.