The fighter was among rescuers who evacuated bodies while troops cordoned off the zone. He spoke on condition of anonymity for fear of reprisals, The Associated Press reported on Friday.
Friday's attack was the latest in a string of assaults blamed on Boko Haram extremists who have indiscriminately killed Christians and Muslims they accuse of not following their radical version of law.
The fighter said there appeared to be only one suicide bomber though "we all heard two explosions" around 5 am in a mosque in the Jiddari Polo area of Maiduguri, the biggest city in the northeast and birthplace of Boko Haram.
Suicide bombers have killed hundreds in recent months.