Roads in the area were also closed, which affected access to Gunwharf Quays.
"This meant that vessels entering and leaving Portsmouth International Port were suspended for a short period of time".
The 500lb bomb was found during dredging work for the Royal Navy's new aircraft carriers, one of the several pieces of unexploded ordnance found since work started to deepen the harbor.
The harbor is now being prepared for the arrival of a new 65,000-ton (metric) aircraft carrier and the unexploded bomb was found in the early hours of Wednesday morning by a ship dredging at the entrance to the busy port.
In a statement, the Royal Navy said the bomb was found in the early hours of this morning.
The unexploded Second World War shell found at Portsmouth Harbour, leading to Wightlink disruption for Isle of Wight travelers.
Pictures of the device posted online by the Royal Navy show a rusted metal shell, identified as a German SC250 explosive.
Divers from the Southern Diving Unit 2 towed the bomb away from the harbor, lowered it to the seabed and planted explosive charges to begin a controlled detonation.
'As always, the Royal Navy stands ready to respond to these call-outs and keep people safe.
"These bombs are still risky despite being several decades old and sitting at the bottom of the seabed for such a long time", said Capt. Roger Readwin of the Royal Navy. "Despite being old, these devices can pose a very serious threat".
The device was caught in the excavator head of a dredger clearing a path into the nearby naval base deep enough for the next generation of aircraft carriers.