The 500lb (250kg) device was found on a building site in Grange Walk, Bermondsey on Monday.
Two primary schools were closed and hundreds of homes were evacuated as a precaution.
A cordon and 656ft (200m) exclusion zone was lifted at about 18:15 GMT as the bomb was removed to a quarry in Kent to be detonated, police said.
The Metropolitan Police force said the device was a 'SA' 250kg WWII German air-dropped bomb, known to the Army's Royal Logistic Corps bomb disposal experts.
Southwark Borough Council thanked people affected by the disruption for their patience.
Earlier the Met's Southwark Borough police tweeted an apology for its "blunt" leaflet urging people to leave their homes as a safety precaution.
The flyer said: "If the bomb explodes buildings in the 200m zone will be significantly damaged and those close to the bomb will be destroyed.
"Remaining in your home is placing your life at significant risk."
Southwark ward councillor Lucas Green said the council had rehoused about 100 people who were unable to return to their homes on Monday night and the Red Cross had helped to provide them with food and supplies.
London Fire Brigade said that between 2009 and 2014 it was called to seven unexploded Second World War bombs and five unexploded hand grenades.
An unexploded World War Two bomb found in south London has been driven away safely under police and Army escort.