The ICC, based in The Hague, was set up to try individuals for the most serious international crimes.
The winner was chosen on Thursday by Parliament President Roberta Metsola and the leaders of its political groups.
The Social Democrats, the second-largest bloc in the chamber, nominated the court, saying they wanted to support it and defend the international order in the face of US sanctions on ICC judges and prosecutors.
Announcing the decision, Metsola said "the EU is built on respect for multilateralism and international institutions," and that the prize "recognises the important work of the court in upholding international law and justice."
ICC President Tomoko Akane thanked Parliament, saying the award came as the court faced "unprecedented challenges," including US sanctions aimed at hampering its work.
US authorities say the institution has become politicised and has sought to unlawfully and unfairly pursue Americans and Israelis on war crimes charges.
European Commission President Ursula von der Leyen welcomed the award, saying the ICC must be free to carry out its mission independently, without pressure or intimidation.
Polish MEP Michał Wawrykiewicz, of the ruling Civic Coalition (KO) party, who backed the nomination, said the court was a key part of the international legal order, above all for holding Russian perpetrators to account for what he described as "genocide in Ukraine."
He called the US sanctions deeply worrying, "an attack on judicial independence," noting similar action from Russia after the court issued an arrest warrant for Vladimir Putin.
The other finalists were Tanzanian opposition figure and lawyer Tundu Lissu, who is currently in prison and campaigned for free and fair elections, and Iranian sisters Taraneh and Romina Rahimi, who are being persecuted over their role in anti-government protests.
Metsola said one of the sisters faces the death penalty and the other decades in prison, and she paid tribute to all three finalists.
The prize will be presented at a ceremony on 16 December.
Last year’s laureates were Andrzej Poczobut, a journalist and activist for the Polish minority in Belarus, and Georgian journalist Mzia Amaglobeli.
The Sakharov Prize, awarded annually since 1988, is the EU’s highest human rights honour.
(ał)
Source: PAP