Yusuf was captured after the military stormed his compound and a mosque in Maiduguri, in Borno state. Yusuf was paraded before local journalists after his capture.
Several hours later, he was dead, supposedly shot while escaping. The New York-based Human Rights Watch called for an investigation into Yusuf's death, saying it believed it to be unlawful.
Yusuf's Boko Haram, which is called the Nigerian Taliban and was formed in 2002, seeks to impose sharia, or Islamic law, across the whole of Nigeria and is also opposed to Western education.
Boko Haram launched a series of attacks on police stations last Sunday. President Umaru Yar'Adua, who is himself a Muslim from the north, authorised the army to take whatever action was necessary to restore order.
The police and army quickly struck back with brutal force, and the majority of those killed were reported to have been militants, although civilians were also among the dead.