Croatia's Prime Minister decided to allow migrants to continue their journey, conceding that closing the border was not a solution.
And as the EU works to prevent the traffic jam of people, its plan to work with Turkey to slow the pace of new arrivals has hit another hurdle.
As many as 3,000 thousand migrants had been stranded in the mud and rain for two days, when Croatia reopened its border with Serbia.
UNHCR spokeswoman Melita Sunjic says migrants rushed across the border, when the gates were suddenly opened.
"When the border opened everybody rushed and here was one young man left who had one leg, so we got a wheelchair and helped him across. That was very moving scene."
Croatian Prime Minister Zoran Milanovic announced earlier he would allow migrants to pass through, saying he realised closing the border was "no solution".
"Obviously, yesterday we kept five to six thousand people on the other side, in Serbia. It's apparent that this is no solution, so we will let them through, we will send them towards Slovenia."
It's Hungary's closure of its southern border with Croatia at the weekend, causing many people to divert to Slovenia.
The UNHCR has warned the migrant crisis cannot be solved by one country opening its doors as another one closes them.
Meanwhile, the EU's efforts to entice Turkey to cooperate in its solution to the migrant crisis appears to have hit a hurdle.
Turkey is calling for new funding from the EU in exchange for stopping the migrants streaming towards Europe
EU leaders at a summit in Brussels last week said they had agreed to an action plan with Turkey, including funding towards camps.
German Chancellor Angela Merkel said leaders had discussed a figure of about AU $6 billion for Turkey.
But Turkish Prime Minister Ahmet Davutoglu says that money should not come out of the funds already earmarked for Turkey as an EU membership candidate.
He says Turkey will not become what he calls a "concentration camp" for migrants.
"Therefore, we would never accept a deal assuming: 'we gave this money to Turkey so the refugees should stay there.' And I told this to Ms Merkel. Nobody should expect Turkey to become a country housing all migrants, like a concentration camp. But illegal immigration should become legal and should be kept under control."
Meanwhile, UN Secretary General Ban Ki Moon has visited a refugee housing centre in Slovakia.
He's calling on countries not to forget the human element of the crisis.
"This migrant and refugee issue has become a global issue, global challenge. I know that each and every country has a very serious political, economic, social challenges in accommodating these people, but at the same time we should know that they are people who are fleeing the war and persecution and very difficult hardship they can never bear by themselves."
