Letters implementing the transit agreement were exchanged between Jaap de Hoop Scheffer, Nato's secretary-general, and Sergei Lavrov, Russia's foreign minister.
A Nato spokeswoman said: "It's been done. It will cover land transit of non-lethal equipment. Air transit is not for today."
The spokeswoman said non-lethal supplies covered everything from food to certain military equipment.
She did not say why troops or air transit would not be covered.
De Hoop Scheffer had said last month that negotiations were taking place on land and air corridors for troops and equipment, plus the possibility of boosting existing co-operation on training local counter-narcotics officials.
Meanwhile, de Hoop Scheffer said talks with Putin on Friday had been positive, but yielded no major breakthroughs on the two sides' disputes.
Following an hour and half of discussions with the president, de Hoop Scheffer said: "The talks were in a positive spirit. I cannot report that this morning we saw stunning breakthroughs."
Putin said he had been encouraged that the United States had listened to Russian concerns about its planned US missile shield system to be deployed in the Czech Republic and Poland and said discussions would continue.
He said: "What is positive in today's dialogue is that our concerns about ensuring our own security... have been heard.
"The visit to Russia [earlier this year] of the US defence secretary [Robert Gates] and the US secretary of state [Condoleezza Rice] showed that our US partners are thinking about measures to improve confidence and transparency and that work will continue."
Alan Fisher, Al Jazeera's correspondent in Bucharest, said: Vladimir Putin was very clear there are some stark differences between Nato and Russia.
"But he also made it clear there is no reason why Nato and Russia cannot cooperate on the missile defence system."
Putin also said he saw no possibility of a new Cold war because "it's in nobody's interests".
However, one source in the Russian delegation at the summit, said Putin had challenged US policy towards Iran during the meeting and said that the country should be helped to emerge from isolation, instead of being threatened.
The source quoted Putin as having said: "No one can seriously think that Iran would dare attack the United States.
"Instead of pushing Iran into a corner, it would be far more sensible to think together how to help Iran become more predictable and transparent."