Frustrated commuters found their journeys disrupted following signal failures and a person falling ill.
Trains were unable to stop at Wandsworth Common station, with passengers being diverted to catch another train from Balham.
A passenger was also taken ill shortly afterwards at platform 12 in Clapham Junction station, which caused further delays.
A spokesman for Southern Trains said: "We are now running again on all lines and there will still be delays of up to 30 minutes while the service returns to normal.
"We apologise for the inconvenience this has caused."
Twitters users were venting their anger about the journey online.
Chris Connon wrote: "These trains are crazy. Currently reversing from Wandsworth to Balham, apparently we skipped our signal."
Katy Clemmans posted: "Why is my train stuck at Wandsworth when all other trains are passing through in London direction? Seriously angry."