The 500-kilogramme German bomb was found early on Sunday morning in King George V Dock, during planned works close to London's most central airport.
As bomb disposal experts from the police and Royal Navy worked to move the unexploded ordnance, the airport was shut down and two successive exclusion zones imposed.
London City Airport chief executive Robert Sinclair announced flights would resume today after the bomb was successfully removed from the dock.
"The exclusion zone has now been lifted and the airport will be open as normal on Tuesday," he said in a midnight statement.
Yesterday's shutdown affected up to 16,000 passengers who were due to fly from London's fifth-biggest airport, although some airlines switched their flights to the city's other hubs.
London City Airport opened in 1987 in the disused docklands. It handled 4.5 million passengers in 2017 and is mainly used by business travellers.
The bomb disposal operation initially saw the evacuation of up to 500 residents, who were allowed to return to their homes on Monday evening while others were evacuated from another area after the 1.5-metre shell was moved within the dock.
Removal of the fused device had depended on the tides, which left authorities waiting until around midnight before they could transport the bomb further along the River Thames to be safely dealt with.
Jonny Campbell, the naval officer in charge of the bomb disposal divers, said the ordnance would be towed along the river after being removed from the sea bed.
"We will then attach high-grade military explosives before carrying out a controlled explosion," he added.
London was heavily bombed during the "Blitz", the Nazi German air attacks of September 1940 to May 1941.
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