Barroso spoke in Rome shortly after Iraqi authorities confirmed they had hanged Barzan Ibrahim al-Tikriti and Awad al-Bandar, two former top officials in Hussein's regime.
"We consider that a man does not have the right to take the life of another man," Barroso said. "It's a fundamental question. I believe in our European values and I take this occasion to thank Italy for all the initiatives that it announced so that, in the framework of the United Nations, we can work together to put an end to the death penalty."
London-based human rights group Amnesty International called the execution brutal and cruel.
And in Iraq, a prominent Sunni group, the Association of Muslim Scholars, said it suspected the execution was a politically motivated act of revenge.
But hundreds of Shi'a took to streets with drums in the holy city of Al-Najaf to celebrate the occasion.
The U.S. Ambassador in Baghdad, Zalmay Khalilzad, said the execution was an entirely Iraqi affair.
(compiled from agency reports)