Jose Manuel Barroso did not say however when the "strategic" document to restart talks would be signed.
He also said the European Commission was ready to send a delegation to Moscow at the beginning of next year so that top level contacts could be resumed.
Attending the summit, Russian President Dmitry Medvedev hailed the end of the delay in the talks. Negotiations were frozen amid a diplomatic row caused by a five-day war between Russia and Georgia over breakaway South Ossetia in August.
Western powers were initially critical of Russia's reaction to Georgia's attack on the breakaway republic, but this stance has softened of late.
The 27-nation European bloc said on Monday that talks on a partnership agreement would resume later this month, despite opposition from Lithuania.
"The conflict in Georgia has emphasized the crucial need for permanent political dialogue between the EU and the Russian Federation, while the global economic crisis has underlined once more the interdependence between the EU and Russian economies," Barroso said before the summit.
