The court has "maintained" the death sentence for genocide and torture against 66-year-old Salahuddin Quader Chowdhury, Chief Justice Surendra Kumar Sinha, the first Hindu to head the top court in the country said, upholding a 2013 verdict by the International Crimes Tribunal.
"The verdict has fulfilled our expectations," said Attorney general Mahbubey Alam.
Defence counsels said they were disappointed with the judgement and planned to seek a review by the top court itself after the full text of the verdict was released by the Appellate Division of the Supreme Court.
Prosecutors earlier described Chowdhury as a merciless killer who murdered more than 200 Hindus, including Singha, the owner of well-known herbal medicine company dragging him out of his prayer room to be shot by the Pakistani soldiers.
This was the fifth time the Appellate Division delivered a verdict on an appeal against a tribunal's judgement.
Chowdhury is the second former minister to have the death sentence upheld after Jamaat-e-Islami's Ali Ahsan Muhammad Mujahid, who has already been hanged.