They also said that only a political process led by the different Syrian groups and supported by the UN can hope to end the war.
The conflict has cost the lives of 400,000 people, many of them women and children, and left 13.5 million people in urgent need of food, water and shelter.
In a resolution adopted on Thursday, MEPs endorsed the EU strategy for Syria and advocated for a united and independent country.
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The EU, as the largest donor, needs to involve itself more in the Syrian peace process, said the resolution.
This includes facilitating a political transition, bringing parties closer together, supporting the Syrian population and preparing for reconstruction.
They also gave support to confidence-building measures, such as unhindered humanitarian access throughout Syria, the end of all city sieges and the release of hostages.
MEPs condemned the forces of the Assad regime, supported by Russia and Iran, as well as by ISIS and Jabhat Fateh al-Sham, and called for a Syria war crime tribunal to be set up.
Meanwhile, UN Secretary General António Guterres, in a speech to MEPs in Strasbourg, also addressed Syria and other similar conflicts.
Guterres said that a “strong and united Europe is an absolutely fundamental pillar of a strong and effective United Nations.”
The Portuguese UN Secretary-General, the first European UN chief since Austria’s Kurt Waldheim in the early 1980s, said global challenges such as the multiplication of conflicts, a human rights violations, climate change and globalisation required the EU and the UN to work together.
In his speech, Guterres expressed his gratitude and appreciation for the EU's commitment to multilateralism and its contributions to development cooperation and humanitarian aid.
He said, “The European Union is clearly the most successful project of peace sustainability in the world since the beginning of history."
The UN Secretary-General addressed a number of issues, notably Syria, migration, globalisation and the need to preserve cultural diversity.
It was the first time Guterres has addressed the European Parliament as UN Secretary-General since succeeding Ban Ki-moon on 1 January 2017. Guterres was UN High Commissioner for Refugees from June 2005 to December 2015 and Prime Minister of Portugal from 1995 to 2002.
Speaking in the same debate, Parliament President Antonio Tajani pointed out that both the UN and the EU were created after the Second World War “to ensure peace and prosperity through a multilateral cooperation”.
“Together, we have to find political solutions to the conflicts in Syria, Libya, and Yemen and to address Isis," he said.
“Together, we need to have to defend the dignity and freedom of people, give perspectives to the new generation and put into practice the agenda 2030.”