The vote was initiated by the opposition New Democracy party, which blamed him for making too many concessions over the agreement, but repelled by Tsipras supporters.
During the vote, thousands of Greeks gathered outside the parliament building, urging the Prime Minister to resign.
READ MORE: Greek Police Use Tear Gas on Protesters Against Macedonia Deal — Reports
The no-confidence vote initiative failed to reach its goals as Tsipras government has 154 out of 300 in the parliament.
Greece and Macedonia have been at a dispute over the name of the Republic of Macedonia. Greece regards "Macedonia" as a term referring to one of its northern regions and the ancient Kingdom of Macedonia, and insisted on the use of another name for its northern neighbour.