The suspect, a Jordanian of Palestinian origin, was flown overnight to New York from Jordan. Investigators believe he drove the rented van that was packed with explosives and was detonated in the basement garage of one of the centre's two towers.
Jordan's Justice Minister, Hisham Al-Tell, identified the new suspect as 24-year-old Iyad Mahmoud Ismail Najem. He was arrested on 31 July in Jordan, one day after the government received an extradition request from the United States.
Mr Najem pleaded not guilty to conspiracy charges in a five-minute hearing at Manhattan Federal Court. He was ordered to appear again on 16 August.
Last year, four men were found guilty of setting off the explosion and sentenced to a total of 240 years each in prison. Earlier this year, the US extradited Ramzi Ahmed Yousef from Pakistan. The alleged mastermind of the attack, he is still awaiting trial.
Janet Reno, the US Attorney General, welcomed the capture of Mr Najem yesterday and acknowledged Jordan's "excellent assistance".