Around 300 people were on board the 4.54am service from Basingstoke and there was only one minor injury reported.
Passengers reported a large emergency response as they waited to be evacuated after the rear axle of the last coach derailed at shortly before 6am.
Lines were reopened after about an hour, but disruption was expected until the end of the day. Trains between Wimbledon and London Waterloo are affected.
At 7.30am, Transport for London (TfL) said some London-bound District line tracks remained blocked and tickets were being accepted on other routes.
Passenger David Holman wrote on Twitter: "Train just shaken violently in a train derailment outside Wimbledon.
"Carriage eight of eight-car train derailed all in carriage shaken violently, stopped by Waitrose, car park full of fire engines. Waiting to be evacuated.
"No apparent injuries, most emergency services here now."
He posted a picture of emergency services in a nearby car park working to evacuate passengers from the train.
Fire brigade cut hole in fence, bridge built to evacuate shortly #derailment pic.twitter.com/33DeJWlA4k— David Holman (@dmh2174) November 6, 2017
@SW_Help @districtline Trains at Wimbledon delayed 4 overland, cancelled for district line @ present. Broken train on track pic.twitter.com/hUyzrx5RE8— Gareth Edwards (@geeedwards83) November 6, 2017
Bloody hell derailed train at Wimbledon.. everyone’s safe 🙏🏼 pic.twitter.com/KFAf8KMojC— Thea Butler (@TheaEsme) November 6, 2017
Thankfully doesn't look like anyone hurt in train derailment this morning near Wimbledon #southwesternrail #trainderailment #commute pic.twitter.com/7RFK6HOhMv— tim hulbert (@timhulbert3) November 6, 2017
THINK YOUR FRIEND WOULD BE INTRESTED? SHARE THIS STORY USING ANY OF THE SHARE BUTTON BELOW ⬇ PLACE YOUR TEXT ADVERT BELOW:>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>The derailed train at Wimbledon. 300 passengers are now being able to leave the area with only one minor injury. @BBCRadioLondon pic.twitter.com/YU5EuqVX8d— Jason Rosam (@JasonRosam) November 6, 2017