The owners of Tazreen Fashions, Delwar Hossain and his wife Mahmuda Akter, were sent to jail after being refused bail. They were among six fugitives wanted in connection with the fire on the outskirts of the capital, Dhaka on November 24, 2012.
Many of those who died in the multi-storey building perished because supervisors ordered workers back to their stations even as an alarm rang and smoke rose through an internal staircase.
A state prosecutor, Anwarul Kabir, said the couple had pleaded for bail after surrendering. He said: "The court sent them to jail after rejecting their bail petition.
Witnesses said several hundred people gathered at the court and chanted for the pair to be given the death penalty. If convicted, they could face life in prison.
In all, 13 people were charged in connection with the disaster, a rare step in a country where critics complain that powerful garment industry bosses often go unpunished for factory accidents.
Bangladesh, the world's second-largest apparel exporter after China, in December raised wages for garment workers and allowed them to form trade unions in July after a string of factory accidents.