They were waiting patiently to be processed by the Albanian authorities, who had suddenly decided to add to the misery by taking the name of every refugee crossing, instead of waving them through as they had been doing since the exodus began on Saturday.
After her lightning visit by helicopter, instead of the arduous seven- hour road trip, Ms Bonino and her entourage departed for further meetings with UN officials about the refugee crisis.
The pitiful exodus continues from Kosovo, with no mercy shown to the old, the sick, nor the poor, as they pour out of the embattled province under the vicious Serb promise - Albania or death.
The border crossing is now split into two lanes, with cars on the right, pedestrians on the left. With at least 100,000 people said to be jamming the road, there was no let-up in sight.
Enver Doda left Pristina, 120km away, at 10am on Wednesday and arrived in Albania 29 hours later.
"The police organised the trip straight to Albania - they didn't let us go anywhere else. I did not want to leave Kosovo but I had to because of the police," he said.
"They came banging on the doors and shouting, and saying if we don't leave now a bullet is waiting for us - either Albania or death."
Thousands of refugees who had walked for hours were slumped in a grassy field just beside the border.
They were mostly women and children, bundled up in brightly coloured jackets and carrying pathetic items of luggage - clothes wrapped in blankets, or bulging plastic bags, or the odd suitcase carried on the shoulder.
They were waiting for some kind of transport out - but it was in short supply.
Where were the buses and mini-vans that in previous days, had shipped refugees out at the government's expense? "Ask the UNHCR [United Nations High Commissioner for Refugees]," said one Western official, grimly.
The few foreign aid workers who are already in place at the border crossing have expressed anger and distress at the delay in setting up proper facilities for the refugees. It seems to have taken an inordinately long time for the international aid agencies to grasp the scale of the crisis, despite the fact that it was obvious to many observers that Albania - and the main road crossing at Morini - would be a prime destination for Kosovars expelled by the Serbs.
Aid workers from smaller aid agencies handed out small jars of baby food - peach puree - to bemused refugees walking over the discarded wrappings of emergency rations that are now depleted.
As a result of the delays in passing the border, at least one refugee died of exposure. The body of Rexhep Nimani, 72, lay cradled in his widow's arms, in the back of a tractor-trailer loaded with 35 children.
"He died today, at about 8am," said a friend, Skender Mauriqi. "He was not sick but it was very cold. We stayed outside all night in the rain.
"We left Pristina at 1pm yesterday. All the way, he kept saying that he wanted to go back..."
Nehad Cetaku, an electronics graduate forced under the Serbian system to work as a mechanic, was desperate to get his pregnant wife, Rabija, into hospital, as she is due to give birth within 48 hours.
"We left Pristina because we had to leave Pristina. They gave us about five minutes to leave our houses, saying if we do not do this, we take a bullet," he said wryly.
Valbona Bajgora, whose family had not eaten for three days because they were too frightened to leave home until forced out by masked gunmen, said many of those expelled from the capital were told to gather at the train station.
"The whole of Pristina was there," she said bitterly. From there, they were taken by bus to the village of Zur, and made to walk to the border. "One of my Serb neighbours arrived the moment I went down the stairs, and followed me out carrying my television and my video," she added.
But others, rather than taking advantage of the anarchy, tried to help.
"I saw some Serb neighbours who were crying, looking at us leaving. One Serb who lives near the mosque came out, begging the soldiers not to kick us out," Mr Mauriqi said. "But they were shooting in the air. Just like in Hitler's time. I never thought I would live long enough to see this."