The line was closed from Paddington to Abbey Wood for a period as technicians raced to sort the problem.
Heathrow travellers faced further woes as the Piccadilly line was also without service between Hammersmith and Acton Town due to a signal failure.
A disgruntled commuter, who wished to remain anonymous, told the Standard: “I was heading into work for a 12pm start – I work US hours – and Woolwich was absolutely rammed with people outside. I use the Elizabeth line almost every day and it’s usually reliable so this is disappointing.
“I had to catch an Uber which means I had to spend a lot more money to get to work. It’s a hassle but I just hope the issue is sorted soon.”
The TfL website said of the Elizabeth line earlier on Friday: “No service between Paddington and Abbey Wood, while we fix a faulty train at Bond Street. SEVERE DELAYS on the rest of the line. London Underground accepting their tickets via any reasonable routes.”
It also warned of “severe delays” on the Picadilly line, adding: “Piccadilly Line: No service between Hammersmith and Acton Town and between Rayners Lane and Uxbridge due to a signal failure at Acton Town.
“SEVERE DELAYS between Acton Town and Heathrow Terminals / Uxbridge. MINOR DELAYS on the rest of the line. Tickets are being accepted on Elizabeth line, Great Northern, London Overground, South Western Railway and Buses via any reasonable route.”
Minor delays have also been reported between Edgware and Golders Green on the Northern line after a dog ran onto the track.