SP Ravindra Sengaonkar and senior police inspector Shrikant Pingle have been suspended and a departmental inquiry ordered against them, state Home Minister R R Patil told reporters.
He assured the departmental inquiry would be completed in the shortest possible time.
Patil said Additional SP Sangram Nishandar has been "warned in writing and reprimanded" for dereliction of duty.
"Wrong sections were applied against the girls. There was no need to take hasty action (against the girls)," Patil said.
He said senior officers will probe what charges could be dropped.
Earlier, the Bombay High Court transferred judicial magistrate R G Bagade who had granted bail to Shaheen Dhada and Renu Srinivasan, who were arrested last Monday after the former posted a Facebook status lamenting the November 18 shutdown and the latter "liked" it.
Though Dhada had not named Thackeray, a local Sena leader complained against the girls and police arrested the duo on November 19, sparking an outrage. A hospital owned by Dhada's uncle was also vandalised despite the girl apologising for her post.
The arrest had set off a debate with some legal experts maintaining that instead of enlarging the girls on bail, Bagade should have discharged them from the case as they had been booked under wrong sections. (More)