The summit's agenda of foreign policy, economic and trade issues was overshadowed by a lunchtime dispute between Sarkozy and European Commission president Jose Manuel Barroso.
Viviane Reding, chief justice of the EU, had insinuated and later retracted that the return of planeloads of Roma to Romania and Bulgaria smacked of World War II scenarios.
Reding retracted the statement prior to the meeting, but that did not stop Sarkozy from calling the remark "a historical shortcut that profoundly hurt the French.
"These words were deeply hurtful," said the French president. "My duty as head of state was to defend France."
Sarkozy denied he had argued with Barroso, but several sources confirmed the dispute.
Luxembourg prime minister Jean-Claude Juncker said "it was a testosterone-heavy exchange" and Bulgarian Prime Minister Boyko Borisov described it as "fierce".
Another source said Barroso "vigorously defended" the role of the commission to apply EU laws governing the freedom of movement for all citizens.
Barroso himself refused all comment, but followed the summit with the statement condemning the French government's actions.
"Discrimination against ethnic minorities is unacceptable," he said.
Despite it all, Sarkozy said French authorities would continue to dismantle "all illegal camps," whoever they belonged to.
German chancellor Angela Merkel agreed Reding's comment was inappropriate, describing the historical parallel as "unfortunate", while British prime minister David Cameron said he was "shocked."
Hoping to stem the rift, EU president Herman Van Rompuy called for mutual understanding. "The relationship between states and European institutions must be based on respect," he said.
Barrosso also conceded Reding's comments were "excessive", but pointed out she had admitted it.
Reding said that she "in no way wanted to draw a parallel between World War II and the actions of the French government today."
Italian Prime Minister Silvio Berlusconi, whose own government came under fire from the commission in 2008 when it started to register and fingerprint Roma living in camps, attempted what he may have considered a more diplomatic approach.
"The problem of the Roma concerns every country in Europe," he said.