"The Nato-Russia Council will meet on an informal basis to re-engage and to have discussions on the issues on which we will agree and, I would also like to add, on the issues on which we disagree," he said.
US Secretary of State Condoleezza Rice, attending her final Nato meeting, insisted "this is not business as usual" and that she still considered Russia's action in Georgia in August to be "unacceptable".
She added: "This is not about competition and conflict and domination, but rather about co-operation in a framework in which one treats one's neighbours, even if they were once a part of the Soviet Union, as equals in the international system."
Russia's permanent representative to Nato, Dmitry Rogozin, welcomed the decision and said his country was ready for dialogue.
"It is now clear that Nato has accepted the reality that has been shaped by Russia," he said.
Thousands of Russian troops are still stationed in Georgia's rebel regions of South Ossetia and Abkhazia.
On Tuesday, Georgian President Mikhail Saakashvili warned the West of "grave risks of returning to business as usual" with Russia without holding it to account for its actions in Georgia.
"If the international response is not firm, Moscow will make other moves to redraw the region's map by intimidation or force," Mr Saakashvili wrote in an article in the Wall Street Journal.
Nato was deeply divided on how to proceed following the conflict in August and had to sidestep some bruising internal debates to reach the day's decisions, correspondents say.
While the US and newer Nato members, from the former Warsaw Pact, are keen to draw Georgia and Ukraine closer, others like Germany and France are wary of antagonising Russia, a key energy supplier.
Nato also does not want Russia to think it has a veto over who joins the alliance, the BBC's Caroline Wyatt says.
The war also raised doubts among many members over whether Georgia, with its disputed territories, was ready to join the bloc or remained too volatile.
Ukraine, meanwhile, has been beset by political turbulence, with the country split on Nato membership.
Correspondents says it will be a struggle for the alliance to prevent divisions on the issue hardening into permanent fault lines.
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