Flights resumed as normal after scores were cancelled when a 500kg explosive was found 15m underwater in the River Thames.
The 1.5m tapered-end shell was moved to a secure location by Royal Navy divers overnight and is now due to be destroyed in a controlled explosion.
A 214m exclusion zone was set up after the German general purpose bomb was found grounded in the seabed at King George V Dock in east London.
Robert Sinclair, chief executive of London City Airport, said: "The World War Two ordnance discovered in King George V Dock has been safely removed by the Royal Navy and Met Police.
"As a result, the exclusion zone has now been lifted and the airport will be open as normal on Tuesday.
"I would like to thank the Royal Navy, Metropolitan Police and Newham Council for their professionalism and expertise in bringing this incident to a safe conclusion."
Lieutenant commander Jonny Campbell, who is in charge of the diving unit disposing of the ordnance, said it will be exploded underwater.
"We assess that we've got good control, that the bomb is in relatively good condition," he said.
"We want to take it away and remove it, but we want to make sure it's done properly."
Unexploded World War Two bombs are occasionally found in the UK and their discovery triggers a military response.
The German Luftwaffe dropped about 25,000 tons of bombs on east London's Royal Docks during the Blitz, according to the Royal Docks Management Authority.