Lawmakers voted 153-140 to back the North Atlantic Treaty Organisation protocol that must now also be approved by all other alliance members.
Opposition parliamentarians argued that Greece had given too many concessions to soon-to-be North Macedonia, including a vow not to oppose its proposed NATO membership.
Greek approval of FYROM's North Atlantic Treaty Organisation accession bid is the final step in the deal. He said that his government had "done its patriotic duty" and would be judged by people and history.
Greek Prime Minister Alexis Tsipras (1st R) addresses Greek lawmakers on the Former Yugoslav Republic of Macedonia's (FYROM) NATO accession protocol, in Athens, Greece, on February 8, 2019. "We did what is right", Tsipras told parliament during a heated debate Friday.
NATO's Secretary-General Jens Stoltenberg presided over Wednesday's ceremony a NATO's headquarters, where Macedonia was invited to join the pact.
FILE - Protesters hold a giant Greek national flag during a demonstration against the agreement reached by Greece and Macedonia to resolve a dispute over the former Yugoslav republic's name, in front of the parliament building in Athens, Jan. 24, 2019.
It also exposed old rivalries with Russian Federation, in a region where Moscow jostles for influence with North Atlantic Treaty Organisation and the EU.
Most Greeks were against any agreement that used the term "Macedonia" in the new name, due to the province in northern Greece called Macedonia, which is the birthplace of Alexander the Great.
The neighboring state must now formally request all countries to start using the name "Republic of North Macedonia" from now on, he noted.
"This is the final act of a nationally damaging deed", he said.
Opponents of the historic agreement in Greece believe that the danger of irredentism is not over, as the agreement recognizes Macedonian language and identity for the citizens of the neighboring state, as Mitsotakis noted.