Raj appeared before the court yesterday.
The discharge application submitted by him pleaded that he was not present at the scene of violence and had no role to play in the incident. The next hearing is on July 1.
Thackeray was booked in connection with the attack on the students appearing for the Railway Recruitment Board examination on October 16, 2008.
State Congress unit president Manikrao Thakre told reporters it has been typical of the Shiv Sena and MNS to provoke youth to violence and then its leaders withdraw saying they had no role to play.
NCP spokesman Nawab Malik criticised the MNS president for inciting youth to take resort to violence against those from other states five years ago and then filing a discharge application that he had nothing to do with the violence.
"It is so typical of the Thackerays to spoil the life of local youth for their own political agendas," Malik alleged.