The convoy of more than 200 vehicles was returning from the eastern city of Luhansk, which is held by pro-Russian separatists battling government forces.
Meanwhile German Chancellor Angela Merkel has arrived in the Ukrainian capital Kiev for talks.
On Friday she described the convoy's movement as a "dangerous escalation".
Kiev and Western officials fear the trucks could have contained military equipment to help the rebels, but Kremlin officials say the vehicles were only carrying generators, food and drink.
Observers from the Organisation for Security and Co-operation in Europe (OSCE) said there was no information about what most of the convoy was carrying.
The head of the OSCE mission, Paul Picard, told the BBC that only the first 37 trucks had been inspected by the Red Cross before they set off into Russia.
The lorries had already been waiting at the border for a week, while Russia, the Ukrainian government and the Red Cross tried to come to an agreement on their passage.
The Russians said the convoy started moving because it could not wait any longer, owing to the worsening humanitarian situation in eastern Ukraine, which is held by pro-Russian separatists.
Four months of fighting in the region have left more than 2,000 people dead. More than 330,000 people have fled their homes.
'Violation of sovereignty'
The White House and the Ukrainian government both described the deployment of the convoy as a flagrant violation of Ukraine's sovereignty.
In a phone call, US President Barack Obama and Mrs Merkel said the conflict had "continued to deteriorate" since a Malaysian airliner was downed last month over rebel-held territory, with the loss of all 298 people on board.
Ukraine called the Russian convoy a "direct invasion" of Ukraine.
Nato and the European Union have also criticised what they said was a violation of Ukraine's sovereignty.
Nato officials have accused Russia of building up troops on its border, saying significant numbers of Russian forces are operating within Ukraine, using artillery.
But speaking to the UN Security Council, Russia's UN ambassador Vitaly Churkin accused Western powers of distorting reality.
"Sometimes it reminded me of the kingdom of crooked mirrors because some members of the Council were not concerned about the fact hundreds of civilians are dying."
He said Russia had to act to save perishable goods and that he hoped the Red Cross would help distribute the aid.
"We waited long enough. And it was time to move, and this is what we did," he said.
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