The 500-kilogramme (1,100-pound) 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 on Tuesday 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 (0000 GMT) statement.
"To everyone who has been affected -- whether you were due to fly on Monday, were evacuated from your home or had your commute to work disrupted by the DLR (Docklands Light Railway) closure -- thank you for your patience and understanding," Sinclair added.