Donegall Square West, Wellington Street and Upper Queen Street were closed to traffic and pedestrians due to the alert, following reports of a suspicious object on Tuesday morning.
The alert was centred close to the Danske Bank near City Hall and part of the Christmas market also had to be evacuated.
Police and army bomb squad officers attended and carried out tests on the object, which was found to be a hoax. Security forces have left the scene and cordons have been lifted.
Every hour of Christmas Shopping is vital for City Centre traders and for them to lose three hours because of this ‘elaborate hoax’ is despicable.
Local traders and politicians have condemned those responsible.
Glyn Roberts, from the NI Independent Retail Trade Association, said: "It does Belfast City Centre no favours as a shopping destination when this type of incident occurs."
West Belfast MLA Alex Attwood has said that the actions of those behind the hoax scare "serve no one and no purpose".
The SDLP man added: "The fact that this bomb scare has occurred at the very heart of Belfast city centre at lunchtime, two weeks before Christmas, is a very graphic representation of how anti-citizen, anti-Belfast and anti-democracy those behind this are."
Secretary of State Theresa Villiers, who was visiting Belfast City Hall earlier on Tuesday to sign the Book of Condolence for the late Nelson Mandela, has urged the public to be vigilant.
She met with some of the local traders from the Christmas Continental Market affected by the alert.
These terrorists have nothing to offer the people of Northern Ireland and we will not allow them to create a climate of fear in the community.
Ms Villiers said: "The security incidents over the past number of days in North and West Belfast, and earlier today in Belfast City Centre are absolutely despicable.
"The Chief Constable has assured me that PSNI are doing all that they can to ensure that Belfast is safe for shoppers and the tourists in the run up to Christmas. Belfast and Northern Ireland are open for business which is why I'm supporting the traders in the city centre today," she added.
"I would urge everyone to remain vigilant over the coming weeks. It is vital that the general public work with PSNI to help protect against terrorist attacks other criminality so we all work together to counter the destructive efforts of the small minority intent on causing harm."