Seven separate failures affected Southeastern passengers through London Bridge, which then created overcrowding at Victoria and Canada Water.
Network Rail and Transport for London apologised to customers saying cable damage and signalling problems had caused delays.
Most faults were repaired by 08:00 BST.
Points problems led to suspensions on the District, Circle and Hammersmith and City lines.
Overrunning engineering work and signalling problems resulted in delays of up to 90 minutes for passengers using London Bridge.
It is the latest in a series of problems at the station.
On the Tube, a signal failure, at Edgware Road in north west London, resulted a part-suspension of the District line as well as severe delays on others.
Sasha Simic, who was caught up in the disruption, tweeted: "Nightmare Monday for commuters after underground suffers severe delays."
Another passenger, Warren Geraghty, tweeted: "Delays in and out of Paddington. Tube has "severe delays". I think my commuting days are coming to an end!!"
Both Network Rail and Transport for London apologised to customers.
A Network Rail spokesman said: "The causes were a mixture of cable damage, component and asset failures.
"Many of those faults were repaired before 8am but by that point the damage was done and trains were severely delayed as a result."
Rush hour travellers have had a "nightmare Monday" commute across London after a series of unrelated rail and Tube train delays.