Desperate migrants got face-to-face with police before chanting “We want to leave” and “Germany, Germany” as the tense stand-off threatened to boil over.
Among the frenzy were crying children and babies, with parents holding them in the air in a frantic bid to board trains.
Others began fighting each other.
Travellers from Syria, Eritrea and Afghanistan had camped on the platform of the Eastern Railway Terminus for days and had paid hundreds of pounds for tickets.
Demonstrations flared up after an announcement was made saying services had been suspended and, later, only non-migrants were allowed in the terminal.
“For those refugees who are being persecuted or have fled war, there should be a fair distribution in Europe based on the economic strength, productivity and size of each country”
German Chancellor Angela Merkel
Last week the decomposing bodies of 71 migrants were found in a truck in Austria while at least 2,500 have died trying to cross the Mediterranean Sea this year.
Hungary took the unprecedented step to close the station claiming it was trying to enforce EU law, which says people seeking asylum should make an application in the first “safe” country.
Many migrants are abusing the system by not registering and trying to make it to richer nations such as Germany or the UK.
Angry Syrian refugee Hussan, 47, who was among the chaos, said: “They took €125 (£92) for each ticket to Munich or Berlin, then they stopped and forced us from [the] station.”
Germany is expected to let in 800,000 this year – four times more than the previous 12 months.
Mrs Merkel warned: “For those refugees who are being persecuted or have fled war, there should be a fair distribution in Europe based on the economic strength, productivity and size of each country.”
EU leaders are due to get together for an emergency meeting on September 14.
Meanwhile Labour leadership contender Yvette Cooper said Britain must open its doors to more refugees.
The MP, vying for Ed Miliband’s old job, said Britain must “step up to the plate” and urged people to separate the asylum debate and migration issue.
She said: “This has become a humanitarian crisis on a scale we have not seen on our continent since the Second World War. Yet we seem paralysed to respond.
“It’s immoral, it’s cowardly and it’s not the British way.”