The agreement to demarcate the contested borders was approved by both parliaments last year after three decades of talks.
The ex-Soviet republics of Uzbekistan and Kyrgyzstan have said that they finished demarcating their contested border to end sporadic deadly clashes.
Since the demise of the Soviet Union, parts of the 1,400-kilometre border have been disputed, leading to clashes between local communities over access to water or agricultural land.
"Kyrgyzstan and Uzbekistan have completed their border demarcation process... putting an end to the border issue," Kyrgyz President Sadyr Japarov said Friday.
The agreement -approved by both parliaments last year after three decades of talks- was signed during a visit from Uzbek President Shavkat Mirziyoyev to the Kyrgyz capital Bishkek.
"This is a historic event that our brotherly people awaited for many years," Mirziyoyev said.
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Protests over agreement
Some protests took place in Kyrgyzstan in recent months against the agreement that includes shared management of key water resources.
Authorities in Bishkek detained protesters across several towns and cities, including a military general, a former member of the constitutional court, a former public prosecutor, journalists and activists.
In June 2010 deadly clashes between Kyrgyz and Uzbek communities in several cities in southern Kyrgyzstan -including Osh and Jalal-Abad- killed almost 500 and displaced around 400,000 people.
Kyrgyzstan still shares a disputed border with another ex-Soviet republic Tajikistan. Fighting between the countries left 50 dead in September.
Twenty-one people died meanwhile in protests over self-determination in the Uzbek autonomous republic of Karakalpakstan in July.
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