First Friday prayers in 28 years held in Azerbaijan's Shusha
Uniformed Azerbaijani soldiers participated in the prayers at the historic Yukari Johar Agha mosque, according to a video report by Anadolu Agency.
The prayers were held after an agreement between the conflicting parties stipulated Azerbaijani forces would retain control over areas seized in the fighting, including the key town of Shusha, while Armenia agreed to a timetable to withdraw from large parts of the region.
Nagorno-Karabakh lies within Azerbaijan but has been under control of ethnic Armenian forces backed by Armenia since a separatist war there ended in 1994.
Heavy fighting erupted in late September - the biggest escalation of the conflict in a quarter-century - and has left hundreds, possibly thousands, dead.
Aliyev stressed the importance of the timely establishment of a peacekeeping centre involving Russian and Turkish peacekeepers.
"We have always wanted Turkey and Russia to play an equal role in the Armenian-Azerbaijani Nagorno-Karabakh conflict, and today we have achieved this," he declared.
"Today, during a conversation with my dear brother (Recep Tayyip Erdogan) we also exchanged views on the activities of the Turkish-Russian joint ceasefire control centre. I think this is a very important step," said Aliyev.
"Because there is already a schedule for the withdrawal of the Armenian armed forces from our lands. By the end of this month, they must withdraw from all lands, still occupied. There is a great benefit in creating this centre in a short time."
Russian began deploying 2,000 peacekeepers to Nagorno-Karabakh on Tuesday after Armenia and Azerbaijan agreed a peace deal to end weeks of fierce fighting over the disputed region.
The Moscow-brokered agreement came after a string of Azerbaijani victories in its fight to retake the ethnic Armenian enclave.
It sparked celebrations in Azerbaijan but fury in Armenia, where protesters took to the streets to denounce their leaders for losses in the territory, which broke from Azerbaijan's control during a war in the early 1990s.
Armenian Prime Minister Nikol Pashinyan, Azerbaijani President Ilham Aliyev and Russian President Vladimir Putin announced the deal in the early hours of Tuesday.
Pashinyan described the agreement as "unspeakably painful for me and for our people", while Aliyev said it amounted to a "capitulation" by Armenia.
The full text of the deal showed clear gains for Azerbaijan.
Agencies contributed to this report.