Labour MEP Cyrus Engerer was the only Maltese MEP to vote in favour of a report identifying abortion as a human right.
The non-binding report, by S&D group member Fred Matić, is officially titled: "The situation of sexual and reproductive health and rights in the EU from the perspective of women's health."
Among other things, it calls for universal access to legal and safe abortion, maternal health care and sexual education across the EU.
It also sought to abolish value-added tax on women's menstrual products and that for all barriers to sexual and reproductive health services to be lifted.
In a statement published after the vote, the S&D group said: "Today the European Parliament has finally stood on the side of women and showed governments that are undermining women's rights that we no longer accept this."
Engerer's fellow Labour MEPs Alfred Sant and Josianne Cutajar both abstained while Alex Agius Saliba voted against.
Both Nationalist Party MEPs Roberta Metsola and David Casa voted against.
A total of 378 MEPs voted in favour, 255 voted against while 42 abstained.
Prior to the vote, Engerer said it was "unfortunate" that in Malta, the only focus on the report was abortion.
"The report stresses access to contraception for all, fertility treatments (IVF) for all, care during and after pregnancy, medical access for trans people and rights for intersex people, among others. others," he said.
"I have always fought for civil liberties, equality and accessibility and affordability in healthcare for all - and I will continue to do so."
MEPs said during the debate that too many member states maintained highly restrictive laws prohibiting abortion except in strictly defined circumstances.
This was "forcing women to seek clandestine abortions or carry their pregnancy to term against their will, which is a violation of their human rights".
Matić welcomed the vote and said it marked a new era in the European Union and the first real resistance to a regressive agenda that has trampled on women's rights in Europe for years.
The European Parliament's Committee on Women's Rights and Gender Equality (FEMM) had adopted the report on May 11.
Maltese anti-abortion group Doctors for Life had criticised the report earlier this month, arguing that it had no legal basis. It claimed the report failed to allow for conscientious objection.
Malta has the strictest abortion laws in the EU but in May, independent MP Marlene Farrugia proposed a bill in parliament calling for abortion to be decriminalised.
Doctors for Choice estimates that at least 300 women in Malta have abortions every year, either by obtaining abortion pills or travelling to countries where abortion is legal.
The resolution was also criticised by the Catholic Church's EU Bishops' Conference saying it held a "one-sided perspective throughout, particularly on the issue of abortion".
"We see the unborn child as an independent life created in God's image and owing its existence to His will. The unborn child has a human right to life," a conference position paper said.
An EU parliament resolution is not binding, but serves to apply pressure on EU member states or the European Commission to act more boldly on issues.
The vote came as a row over a law targeting LGBT people in Hungary caused a ruckus at an EU summit, with 17 countries, including Malta, calling on Prime Minister Viktor Orban to scrap the legislation.
Culture wars over gender and sexuality have increased of late in EU politics, often pitting western countries against the more socially conservative nations of eastern Europe.