In a footage released in social media, an Azeri soldier is seen reciting Adhan at the minaret of the mosque.
Shusha is a part of the Karabakh region of Azerbaijan that was under Armenian control for two decades but was recently liberated.
The city is a major cultural and historical place and also has strategic importance for its geographic position.
Leaders of Azerbaijan, Armenia, and Russia signed a statement on ending the war in the disputed Nagorno-Karabakh earlier this week.
Azerbaijan and Armenia had been fighting over Nagorno-Karabakh since September.
Karabakh is internationally recognized as part of Azerbaijan, but it is held by ethnic Armenian separatists backed by Armenia since 1992, when they broke from Azerbaijan in a war that killed some 30,000 people.