The Istanbul-based Orthodox patriarch on Saturday signed the formal decree confirming the creation of an independent Ukrainian church, marking a break with the Russian church that has angered Moscow.
The Ecumenical Patriarch Bartholomew of Constantinople, the leading authority in Orthodox Christianity, signed the decree known as Tomos at a ceremony in Istanbul.
Ukraine's President Petro Poroshenko and former Ukrainian president Viktor Yushchenko were on hand to witness the ceremony.
"Dear Ukrainians, this is a historic event! This is a great day!" Poroshenko said as he thanked the Orthodox patriarch.
"Once more, words of great gratitude in the name of the Ukrainian people, in the name of our nation to Your Holiness... It took us a very long time to get here."
The Ecumenical Patriarchate first agreed to recognise the independence of the Ukrainian Orthodox Church in October. Then in December a historic council of Orthodox bishops in Kiev created the independent body.
The Russian Orthodox Church cut ties with the Constantinople Patriarchate in protest at the move, which dealt a huge blow to Moscow's spiritual authority in the Orthodox world.
Vladimir Legoida, a spokesman for the Moscow church, denounced the decree as "a document that is the result of irrepressible political and personal ambitions".
It had been "signed in violation of the canons and therefore not possessing any canonical force," Legoida added in a statement.
Nikolai Balashov, another senior official for the Russian Orthodox Church, hit out at Ecumenical Patriarch Bartholomew I, saying he had "ended the global Orthodox fraternity and permanently lost the right to be called a spiritual leader".
The Ukrainian church's new leader is Metropolitan Yepifaniy.
Yepifaniy, whose secular name is Sergiy Dumenko, has been a critic of Moscow's religious influence in Ukraine and has supported Kiev's army against pro-Russian rebels.
Ukraine and Russia have been at loggerheads since 2014, when Kiev street protests urging Ukrainian integration with Europe led to the ousting of pro-Moscow president Viktor Yanukovych.
Russia subsequently annexed Crimea and has supported Russian-speaking separatists in Ukraine's east, in a conflict that has claimed the lives of more than 10,000 people.
Regina Elsner, a research fellow at the Centre for East European and International Studies in Berlin, said recognition of the Ukrainian church's independence was only the "first step on a long road".
"We will have to see which Ukrainian bishops will join the new church and which other Orthodox churches will recognise it," she added.