A victorious President Ilham Aliyev said he had achieved a decades-long "Azerbaijani dream" by retaking Nagorno-Karabakh from ethnic Armenian separatists, as he raised his country's flag in the region's main city on Sunday. 

Dressed in military attire, the longtime leader flew the blue-red-green flag in what Azerbaijan calls Khankendi and Armenia calls Stepanakert, cementing Baku's conquest after last month's lightning offensive.

The 24-hour military operation in September led to the exodus of nearly all ethnic Armenians from Karabakh. 

It was the first time Aliyev had set foot in the city since it fell to ethnic Armenian separatists in the 1990s. 

"We achieved what we wanted. We fulfilled the dream the Azerbaijani people have lived with for decades," Aliyev said in a victory speech.  

The vast majority of the estimated 120,000 ethnic Armenians that had been living in Karabakh have since fled across the border to Armenia. Overnight, the main city became a virtual ghost town.

Aliyev said his country has "waited 20 years" to see Azerbaijani rule in Karabakh. 

"This victory will stay in our history forever," he said, triumphantly. 

Aliyev's trip came exactly 20 years after he became president of Azerbaijan, succeeding his father Heydar Aliyev.

The authoritarian leader said he had longed to take control of Karabakh since acceding to power. 

"Twenty years ago, when I began to fulfil my official duties as president, I set myself a number-one task," he said. 

"So that on all territories, on all lands, in all towns and villages that at the time were under occupation, the Azerbaijani flag would fly."  

- Visits towns, fortress -

Baku published images of the longtime leader in military attire on his knees, kissing the Azerbaijani flag before it was raised on a flagpole. 

It said he also visited a reservoir and an ancient fortress, as well as other towns.  

The 61-year-old posed in front of mountains and water, holding pomegranates -- a fruit associated with the region -- in one of the photographs. 

Aliyev's visit came as Pope Francis on Sunday called for the protection of Karabakh's ancient Christian Armenian monasteries and churches. 

The Catholic leader spoke after his traditional Angelus prayer in Saint Peter's Square in Rome: 

"Beyond the humanitarian situation of the displaced people, which is serious, I would like to appeal for the protection of the monasteries and places of worship in the region."

He called on the new authorities and "all inhabitants" to respect the places of worship "in an expression of faith and a sign of a fraternity that allows us to live together in our differences".

Largely Christian Armenia has accused mainly Muslim Azerbaijan of "ethnic cleansing" in Karabakh, which Baku denies. 

Aliyev's trip came after he met Russian leader Vladimir Putin at a gathering in Kyrgyzstan of leaders of former Soviet republics, which Armenian Prime Minister Nikol Pashinyan did not attend. 

While Aliyev did not go to a European summit for talks with Pashinyan earlier this month, his office has said that he intends to travel to Brussels for talks with the Armenian leader. 

Azerbaijan and Armenia have been locked in a dispute over Nagorno-Karabakh since the dying days of the Soviet Union. 

The mountainous region was populated mainly by Armenians and became part of Azerbaijan under Soviet rule, in the years following the fall of the Russian Empire in 1917.

The neighbours went to war twice over the territory, in the 1990s and in 2020. 

bur/gil