Rail engineers have repaired a signalling fault that caused hundreds of football fans to miss the Carling Cup final kick-off.
Fans packed in a carriage on their way back to London
Network Rail apologised for "significant delays". Services finally returned to normal on Monday afternoon.
Arsenal and Chelsea fans heading to and from Cardiff's Millennium Stadium on Sunday were affected by the delays.
Queues outside Cardiff Central railway station took more than four hours to clear after the match.
First Great Western said there were still minor problems late on Monday afternoon and passengers could expect delays of up to 20 minutes.
Monday's First Great Western 0715 London Paddington to Cardiff and 0955 Cardiff to London services were cancelled and other services faced delays.
In addition, services from Portsmouth to Cardiff terminated at Bristol before returning.
An estimated 2,000 football fans missed the start of Sunday's Carling Cup final, eventually won 2-1 by Chelsea.
The match was the last Carling Cup final due to be played in Cardiff
A statement from Network Rail said engineers had worked through the night and would "continue to work throughout today to rectify the problem as quickly as possible."
Network Rail is also investigating the cause of the signalling cable fault, although appears to have ruled out vandalism.
Police said the atmosphere among football fans before and after Sunday's match was largely good natured, however many complained they were not given enough information.
Many more supporters spent much of last night trying to get home after the match.
606 VIEW: Were you involved? Did you miss kick-off?
A serious electrical problem was identified at Newport on Sunday morning, just hours before thousands of supporters were due to travel on the line.
It meant that many spent up to three hours between Bristol and Cardiff, forcing them to take their seats midway through the first half.
Fans heading back to London said it had ruined what may have been the last time they visit Cardiff for a major football cup final.
Although some trains were up to 90 minutes late for the game, football officials ruled the match should still start on time.
British Transport Police said the signalling problem was caused by an isolated electrical problem in the cables at Newport.
Network Rail spokesman Ben Herbert apologised for the delays, which he said had been caused by a "fairly serious" but unforeseen signalling problem.
He told BBC Radio Wales: "We can appreciate it did cause pretty major disruption for a lot of people yesterday and this morning.
"If we had known about it, we would have put arrangements in place, worked with the train operators, to make people aware a lot earlier.
"Unfortunately it is one of these things we could not have foreseen. It was very unfortunate it did coincide with that very big match at the Millennium Stadium."
The match, which ended in a 2-1 victory for Chelsea, was the seventh Carling Cup final to have been held in south Wales during the rebuilding of English football's traditional home, Wembley, in north London.
Football's showpiece games are due to return to Wembley, beginning with the FA Cup Final in May.