The bill, with the backing of Prime Minister, Alexis Tsipras, was passed by 171 votes in Greece's 300-seat parliament, enabling people over the age of 15 to legally change their gender on official documents without undergoing sterilisation.
The Orthodox Church said in a statement that the change in law was "a satanic deed" and would lead to "the destruction of social cohesion and the spiritual necrosis of man".
Previously, those wanting to change their gender on official documents had to undergo sex-change surgery and medical tests.
The change in law brings Greece in line with most EU member states.
During a debate on Monday, Mr Tsipras urged MPs to support the change.
Speaking before the vote, he said: "We are on the side of those who have no voice, or whose voice is stifled.
"What God is it that has us take decisions that push children into [situations of] bullying, humiliation and suicides?"
However, the law change has also attracted strong criticism from conservative politicians who have said the minimum age of 15 is too young.
This was reiterated by the Orthodox Church that said making it easier for people to change their legal gender "torpedoes the sacred institution of the family, contrasts with morality and common sense, and destroys man".
The Church has called for the bill to be withdrawn.
