De Hoop Scheffer gave no date for the resumption of talks, but said it should happen "as soon as possible after Nato April summit", which will mark the bloc's 60th anniversary.
He added that the alliance would be urging Russia to change its opinion on areas of "fundamental differences".
De Hoop Scheffer pointed to Moscow's decision to recognise the breakaway Georgian regions of Abkhazia and South Ossetia following Russia's conflict with Georgia in August, last year.
"We will urge Russia to meet fully its commitments with respect to Georgia," he said.
Neave Barker, Al Jazeera's correspondent in Moscow, said the decision reveals just how vitally important Russia is to Nato.
He said the alliance was pushing "aside a huge disagreement over the recognition of Abkhazia and South Ossetia as sovereign nations by Russia," to address "more pressing issues, particularly the escalation of violence in Afghanistan".
James Nixey, a Russia expert from international relations specialists Chatham House in London, told Al Jazeera the decision would not be welcomed by all Nato members.
"Nato, like the EU, is a situation of nation states, and the ones closest to Russia tend to be the ones most afraid of Russia," he said.
He said the US and Nato were "basically trying to re-set the dial" with Russia, but this would not change "the fact that there really are some very very awkward difficulties between Russia and the West, not least ... Russia's desire to control the regions in the former Soviet space".
Earlier, Hillary Clinton, the US secretary of state, said it was time for Nato to make a "fresh start" with Russia.
"It's time to explore a fresh start. We can and must find ways to work constructively with Russia where we share areas of common interest, including helping the people of Afghanistan," she said.
"It is time to move ahead, not wait in place with the illusion that things will change on their own."
Clinton also urged Nato members to help Ukraine and Georgia find ways to join the alliance.
"We should continue to open Nato's door to European countries such as Georgia and Ukraine and help them meet Nato standards," she said.
Russia strongly opposes alliance membership for the two former Soviet states because Moscow fears Nato is expanding into its sphere of influence.
The agenda of the talks in Brussels will also include examining Nato's mission in Afghanistan.