Jose Manuel Barroso said the era of “limited sovereignty was over in Europe”.
The summit failed to revive an association agreement with Ukraine that was due to be its centrepiece.
Ukraine’s President Viktor Yanukovych said he could not afford to sacrifice trade with Russia – which opposes the deal – for EU ties.
Viktor Yanukovych froze plans to sign Ukraine’s trade deal last week. In Vilnius, he defended his refusal to sign, saying the EU was not offering adequate financial aid.
After the two-day summit, Jose Manuel Barroso said: “We will not give in to external pressure, not the least from Russia.
“What we cannot accept is a condition on a bilateral agreement to have a kind of a possible veto of a third country. This is contrary to all principles of international law.”
EU Council President Herman Van Rompuy said the parties had been “really close” to signing the association agreement, but added that “we need to overcome pressure from abroad”.
“We are embarked on a long journey, helping Ukraine to become, as others, what we call now, <<new member states>>. But we have to set aside short-term political calculations.”
However, progress was made with two other ex-Soviet states, Georgia and Moldova.
Association agreements with both were initialed – a stage prior to signing – on Friday. Diplomats have expressed hope those deals can be signed next year.
EU leaders said in a statement earlier that they “strongly” disapproved of Moscow’s pressure on Ukraine not to sign – while Russian President Vladimir Putin accused the EU of “blackmail”.
Analysts say Russia worked hard to undermine the EU agreement with Ukraine, which it sees as a strategically vital partner.
On the one hand, it offered Kiev loans and price discounts. On the other, it threatened painful trade sanctions and higher gas bills.
On Thursday, Viktor Yanukovych told Ukrainian TV that an EU offer to lend Kiev 610 million euros ($828 million) was inadequate.
He said Ukraine would need at least 20 billion euros a year to cover the costs of upgrading its economy to “European standards”.
“For three years in succession they [EU leaders] have shown this candy in pretty wrapping to us,” Viktor Yanukovych added.
“We don’t have to be humiliated like this. We are a serious country, a European one.”
Meanwhile pro-EU protests are continuing in Ukrainian cities against the government’s decision to back out of the agreement.
Prominent Ukrainian opposition politician Vitali Klitschko, who is also in Vilnius, said he hoped the agreement would be signed after all.
“We Ukrainians want the changes,” the world boxing champion added.
“We want to live with the European family, with European rules, with Europeans’ life standards.”
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