The Oyster card system is back up and running in time for London's afternoon commute home after breaking down during the morning rush hour.
A Transport for London (TfL) spokesman said ticket barriers were now working and any customers accidentally charged a full cash fare would be refunded.
Peter Hendy, Transport Commissioner for London, said the technical fault left him "incandescent with rage".
The latest problem came just two weeks after a similar disruption.
Friday's breakdown, which affected pay-as-you-go Oyster cards across the Tube network from 0600 BST, infuriated Tube bosses.
Mr Hendy said: "We are determined that neither TfL nor Londoners lose a penny from either of these system failures."
TfL said the disruption will cost hundreds of thousands of pounds.
At one point in the morning rush, ticket barriers at all Tube stations were kept open as engineers tackled the problem.
The cards are used as a form of payment across the city on the Tube, buses, trams and the Docklands Light Railway.
But the route home should be problem free for commuters, a TfL spokesman said.
"People should not experience any problems, the fault was solved shortly after 1000 BST today."
The spokesman stressed that customers inadvertently overcharged for not touching in and out on the system did not have to take any action, as their cards would be automatically refunded.
"The message is you don't need to do anything at all if you have attracted a £4 fare, it will be an automatic refund," the spokesman said.
Passengers touch the electronic card on a reader on entry or exit to a station, or when getting on a bus.
TfL said incorrect data used to update cards was sent out by TranSys, the consortium responsible for Oyster, resulting in the failure.
Unlike during the previous disruption two weeks ago, Oyster cards were not believed to have been corrupted as a result of the latest fault. Valerie Shawcross, chair of the Greater London Authority transport committee, said TfL lost "a lot of money" as a result of the problem.
She added: "It needs to be repaid to them. We have to know that this is not going to happen again."
A TranSys spokeswoman said "steps are being taken" to ensure the fault does not recur.
About 17 million cards have been issued since the introduction of the Oyster system in 2003.