"The protestores have been dispersed. The situation has been brought under control and it is peaceful now," Hyderabad police commissioner Anurag Sharma told reporters.
The police was in the process of booking cases in connection with the stone pelting incident.
Sharma said the police were verifying the CCTV footage, he said, adding the action will definitely be initiated against the stone pelters.
"Patrolling has been intensified in all sensitive areas of Old City as a precautionary measure," a police officer said.
Police had already made elaborate security arrangements in Old City, which is said to be a stronghold of MIM following the arrest of Owaisi.
After the prayers, the protesters raising pro-MIM slogans took to streets near Hussaini Alam and Shahalibanda localities demanding the immediate release of Owaisi, who is currently under judicial custody and lodged in Adilabad District Jail.
Police arrested Owaisi, leader of MIM legislature party in the Legislative assembly, from Gandhi Hospital in Hyderabad on January 8 in connection with an alleged hate speech case booked against him by Nirmal Town police.
Owaisi, accused of sedition and criminal conspiracy for his "hate speech" also faces similar cases registered by Nizamabad Town police besides Osmania University police in Hyderabad.