Initially the Coastguard was called in just after 5pm on Friday. Sean McCarry of Belfast Community Rescue Service said the body was found with sonar equipment shortly after 5pm today, Sunday, near Donegall Quay.
Former Belfast Lord Mayor Jim Rodgers said: “This is a terrible tragedy but I am relieved that the body has been found because the family must have been going through a terrible time.”
He commended a civilian who attempted to rescue the man on Friday about 5pm, after which the Coastguard was called out.
“One person entered the water and a second went in to assist,” a spokeswoman for the organisation said.
The second man was helped out of the water and the search for the first continued throughout Saturday, until the body was found on Sunday evening.
Mr McCarry said: “We located the body using side scan sonar, which is specialist underwater search equipment. Then the PSNI dive team went in an recovered the body.”
There had been an ongoing search since Friday evening, involving the Coast Guard, the PSNI and the police helicopter.
“Even though we have no confirmation of the identity we are not looking for anybody else,” he added.
It is understood the PSNI are awaiting for a positive identification from relatives of the deceased.
Mr McCarry said the body was eventually found using specialist equipment which was bought after fund-raising efforts by a family whose son drowned in the Lagan in 2012.
“It is called side scan sonar,” he said. “It basically looks like a torpedo and is towed behind the boat. It was exactly the same equipment used to find the Titanic, supplied by the same company. The only difference was that the version used locally is installed with different software.
“We have recovered quite a few bodies with it.”
It cost over £40,000 which was raised by the family of Joby Murphy, 20, who went missing after a Snow Patrol concert in Belfast in 2012, he said.
Rescue workers used specialist sonar equipment borrowed from rescue services in Mallow in Co Cork to locate him.
Following the tragedy, the Murphys set up an appeal in Joby’s memory. Snow Patrol gave £10,000 towards the equipment.
The Community Rescue Belfast organisation which Mr McCarry works with now uses it on behalf of police, he said.
The service, which is run entirely by volunteers, also used the equipment to find the body of a young west Belfast man near the Queen Elizabeth Bridge in recent times.
It has also lent the device for use in finding bodies in the Republic of Ireland and in England.