Turkey is Azerbaijan's staunch ally and had backed it during clashes with Armenian forces over the disputed Nagorno-Karabakh region which started on September leading to the death of at least 5,000 people.
"Karabakh's freedom will be the beginning of a new era," Erdogan said. "Azerbaijan's saving its lands from occupation does not mean that the struggle is over," the Turkey president said.
Erdogan joined Azerbaijan's President Ilham Aliyev during the celebrations over its victory against Armenia as the army paraded weapons seized from Armenia during the six-week war.
The Armenia-Azerbaijan conflict ended after a peace deal was stuck brokered by Russia in which Armenia ceded control over parts of the Nagorno-Karabakh enclave including seven districts it had seized during the war in the 1990s.
Russian peacekeepers entered the Nagorno-Karabakh later to ensure stability in the region for a five-year period which can be extended later with the peace between the two sides being monitored in Azerbaijan by Turkey's military.
Armenia had earlier accused Turkey of involvement the conflict by pushing foreign fighters which was dismissed by Erdogan's government.
Erodgan has consistently maintained that Azerbaijan's ties with Armenia could only be restored only if Armenian forces withdrew from Nagorno-Karabakh.