"Today's vote closes the most important round of obligations involving Greece", Prime Minister Alexis Tsipras told parliament ahead of the vote.
NATO members signed the accord with Macedonia this week, days after the Greek parliament endorsed an agreement between Athens and Skopje that changes Macedonia's name to North Macedonia.
The vote came after the former Yugoslav republic agreed with Greece previous year to change its name to North Macedonia and following ratification of the deal by the countries' parliaments.
Greece's parliament has approved a measure for Macedonia to join North Atlantic Treaty Organisation, ending a decades-old dispute. "I feel we have carried out our patriotic duty", Tsipras said.
Since 1991, Athens has objected to its neighbour being called Macedonia because Greece has a northern province of the same name. Greek opposition parties said the agreement made too many concessions to Macedonia.
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Until then, the Republic of North Macedonia - as it will soon be - will not have the right to vote at alliance meetings.
On Wednesday, Skopje signed North Atlantic Treaty Organisation accession papers in Brussels that will lead to Macedonia becoming the alliance's 30th member once the bid has been ratified by all members.
Negotiations between Greece and Macedonia were protracted and hard.
Western countries strongly backed the deal between Greece and Macedonia, after the country's bid to join North Atlantic Treaty Organisation had been shelved for a decade and amid European concerns over Russia's vocal opposition to the alliance's expansion further into the Balkans.