Asadul Islam alias Arif, a leader of the Jamatul Mujahideen Bangladesh (JMB), was executed in Khulna jail after the Supreme Court upheld his death sentence in August for the blast.
"He was hanged to death at 10:30 pm," an official at Khulna jail said.
Arif and six other top JMB leaders including its founder Shayakh Abdur Rahman were sentenced to death on May 29, 2006 for killing judges Jagannath Pare and Sohel Ahmed.
Arif, who was absconding was later arrested on July 10, 2007. He filed the petition with the Supreme Court this year seeking review of its judgement.
Bangladesh has blamed the JMB for the July 1 attack on an upmarket Dhaka restaurant in which 22 people, mostly foreign hostages, were killed.
Security forces have since launched a deadly crackdown against extremists linked to the attack.
In August, just weeks after the cafe attack, Bangladesh's highest court led by the chief justice dismissed Arif's final appeal, clearing the way for his execution.
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