De Hoop Scheffer said: "Allies agreed on what I would qualify as a conditional and graduated re-engagement with Russia."
He said operational meetings of the Nato-Russia council, a forum that manages the relationship, would resume informally.
The secretary general said this did not mean Nato had changed its view that Russia had used "disproportionate" force in invading Georgia in August, or that it was acceptable for Russia to threaten to station missiles near Nato borders.
European capitals had urged Nato to consider resuming full contacts with Russia but the United States had been reluctant to make any early move.
Condoleezza Rice, the US secretary of state, had said before the meeting she did not oppose "in principle" reviving contacts with Russia via the Nato-Russia council.
But referring to Russian troops still in Georgian breakaway regions, she said Nato should be very cautious about any move on military co-operation.
Alternative bodies
Meanwhile, the ministers, who were meeting almost four months after Russia's war with Georgia, appeared certain to back away from offering the two hopefuls a fast-track to joining, despite intense lobbying from the US.
Georgia and Ukraine are far from fulfilling Nato's membership criteria, which include political, democratic and military standards and good relations with their neighbours, as well as public support for joining.
The alliance should encourage the two former Soviet republics to carry out much needed reforms, without offering them a membership action plan (Map), the next common formal step for joining Nato.
The Map has been the penultimate membership port of call for candidates since 1999, but it is not a condition for accession, and Washington and its allies believe reform itself is more important than the body under which it happens.
Rice, who is taking part in her last Nato meeting, leads a group of allies who believe that the Nato-Georgia commission and Nato-Ukraine commission are the best forums under which reforms can take place.
Arriving for the talks at Nato's headquarters in the Belgian capital, Franco Frattini, Italy's foreign minister, said: "We have now two new instruments that are the new commissions. If we decide through the two newly established commissions it is much better than insisting on Map, where there are some disagreements.
"The first point is to avoid in any case disagreements and divisions among our membership, otherwise we would give a very bad message to the outside world."
One European Nato diplomat, who wished to remain anonymous, described the two commissions as "very useful vehicles for taking this forward".
Meanwhile, David Miliband, the British foreign secretary, said Georgia and Ukraine "want practical help".
"They know that the immediate issue is actually not a decision today on membership," he said.
"The issue today is a decision on how we help those countries upgrade and develop their own armed forces so that they are able to be a positive presence and a positive force for stability."
Russian relations
However, Germany and France lead a bloc of half a dozen European allies taking an increasingly tougher line against the entry of Georgia and Ukraine.
Relations with Russia, which deteriorated badly after the war, were a key element of Tuesday's discussions.
The Europeans had been particularly keen to foster better ties with Moscow, given its dominant role in providing energy to the continent, and the statement by De Hoop Scheffer appeared to confirm that their views had held sway.
They are also wary of the US tactic to try to by-pass the Map process.
A member of one European delegation, who wished to remain anonymous, said: "Half the motivation of the United States is to punish Russia."
On Monday, a German government spokesman underlined that while Russia should have no veto over their hopes, Nato leaders had pledged in April that the accession of new members "would indeed be co-ordinated with Russia".