The line was suspended in the middle of the morning rush hour, just after 8am, because of a signal failure at Bank, Transport for London (TfL) said.
Update: No service due to a signal failure at Bank.— Waterloo & City line (@wlooandcityline) December 9, 2016
Meanwhile, the District Line had minor delays, while the Piccadilly Line continued to be beset by delays after half its trains were taken out of service.
TfL has said wet Autumn leaves had caused its trains' wheels to lock when braking, damaging both the wheels and the track. A longer-than-usual leaf-fall period this year has meant trains incurred more damage.
More Southern misery
Today Southern bosses also admitted services will be "severely disrupted" next week after the company failed in a High Court bid to prevent Rail, Maritime and Transport workers from walking out.
The company put together a map showing how various routes will be affected. It indicated routes to and from Gatwick Airport, Brighton, Croydon and Lewes will all be hit by the strikes, which begin next week and run right up until Christmas.