SP (Thane rural) Ravindra Sengaonkar and senior police inspector Shrikant Pingle have been suspended in the case, state's Home Minister R R Patil told reporters.
He said action has been taken after obtaining legal advice.
"There was no need to charge the girls under wrong sections," Patil said, adding that there was no need to take hasty action (against the girls).
The girls Shaheen Dhada and Rinu Shrinivasan, both 21, were arrested after Dhada had lamented in a Facebook post the November 18 shutdown due to Thackeray's funeral. Shrinivasan had 'liked' the post.
Though Dhada didn't name Thackeray, the local Sena leader complained against the girls and police arrested the duo on November 19, sparing an outrage.
On November 20, police arrested the vandals who had damaged Shaheen's uncle's hospital on November 18, despite her removing the post and apologising that day itself.