Rail bosses warn disruption across the network could continue into the Thursday morning rush-hour.
London Victoria has been left "at a standstill" because of a "major signal failure" during rush-hour.
Part of the station, the country's second busiest, was closed due to overcrowding fears. Services faced delays and cancellations until the end of Wednesday.
Southern Rail, which operates many of the services, advised passengers not to travel from Victoria.
About 75 million passengers passed through London Victoria last year.
Images posted on social media showed hundreds of passengers held on the station concourse, unable to catch Southern, Southeastern and Gatwick Express trains.
Thameslink services out of London Bridge have also been affected by the problems.
Peter Kyle, the Labour MP for Hove and Portslade, was caught up in the disruption. He described the central London hub as being "at a standstill".
Mr Kyle, said the disruption means he may miss Christmas dinner with his staff.
He tweeted: "I'm sorry to every passenger, I know there's a lot more that needs sorting on this service, I'm fighting for that. You have been let down badly this evening."
"The woman next to me is in floods of tears as she's missing her flight from Gatwick."
Rob Broomby, a TV producer, stuck at Victoria said it was the "worst transport chaos" he had seen.
He added: "There was a lot of good humour in the bar as people settled in for a long wait, but when the platform indicators began flashing on and off it felt more like a Christmas tree with dodgy wiring."
Network Rail apologised and warned that disruption could continue into Thursday morning's rush-hour.
It said: "Some trains will be finishing the day in the 'wrong' place, so we do expect there to be some disruption tomorrow morning as operators move their stock and crew around."
