The Emir of Uba survived the attack.
The Emir of Gwoza, Idrissa Timta, was killed Friday after armed men abducted him and a colleague, local officials said.
Suspected Boko Haram militants attacked and abducted the traditional ruler, and his colleague, the Emir of Uba, Ismaila Mamza on Friday morning.
The two leaders were travelling to Gombe State for the funeral of the of the Emir of Gombe, Shehu Abubakar, who died on Tuesday evening at the Royal Marsden Hospital, London, where he was undergoing treatment for cancer.
After being attacked and abducted, the two emirs who were riding in the same car, tried to escape by fleeing into the bush, officials say.
The Emir of Uba survived the attack, and was later found in the bush by soldiers who had fought the assailants.
It is not clear whether it was the insurgents who killed the emir or security personnel who tried to repel the attackers.
A version of the story said the Emir died of shock as security agents engaged his abductors in a gun duel.
But the body of the Emir of Gwoza, Mr. Timta, was later found, a top security personnel confirmed.
Earlier, witnesses said the two men were abducted on their way to Gombe.
A top security personnel confirmed the emir's death.
"It was really sad that the Emir of Gwoza got killed in the attack; but his colleague, Emir of Uba managed to escape unhurt," the source said.
Local officials who spoke to PREMIUM TIMES said the slain leader may have died of shock as there was no bullet wounds on his body.
Borno state Government officials have yet to issue a formal statement on the incident.
Witnesses said all the vehicles on the convoy of the emirs were also burnt by the attackers.
Officials said the children and family members of the late leader have gone to receive his body for burial in Gwoza.
The two abducted emirs were elevated to First Class traditional ruler status only in January.
The abduction came 46 days after the Boko Haram sect whisked away over 250 schoolgirls from their dormitories in Chibok.
Over 200 of the girls are yet to be freed.