Khalid al-Fawwaz will now stand trial on January 20 over the attacks on the US embassies in Kenya and Tanzania that killed 224 people and wounded around 5,000.
US District Judge Lewis Kaplan postponed the start of the trial, previously scheduled for January 12, during a short hearing that Fawwaz chose not to attend.
Co-defendant Abu Anas al-Libi, who was captured by US troops in Libya in October 2013, died in a New York hospital on Friday. He had been suffering from advanced hepatitis C and liver cancer.
One reason for the delay was the complication of who should present evidence originally due to be handled by Libi's lawyer, Bernard Kleinman.
The federal judge called Libi's death "very regrettable." He praised Kleinman's "commendable job" in caring for his client "virtually to the end."
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"It was a very, very difficult thing to witness and I appreciate the court's condolences," Kleinman replied.
Fawwaz's trial is expected to last more than a month.
Government prosecutors expect to take four weeks to outline their case. Fawwaz's lawyer Bobbi Sternheim said the defense may need less than a week.
Fawwaz was arrested in Britain in 1999 and pleaded not guilty to conspiracy charges over the 1998 bombings.
At the time of his arrest, he was allegedly the head of the British cell of Al-Qaeda. He fought but lost a nearly 12-year battle against being extradited to the United States.
Libi had also pleaded innocent.
A third suspect, Egyptian Adel Abdel Bary, last year pleaded guilty to playing a role in the 1998 attacks.