Dr Joseph Kabungo, a Zambian attending the match as an anti-doping official was a medical officer for both the African confederation (CAF) and global football governing body FIFA.
The Nigerian Football Association said Kabungo's cause of death was a heart attack. A statement circulated in the evening said: "It is a very sad incident and one is shocked that some persons are distorting it terribly and claiming that he was beaten to death by fans; that is a lie: He died after a sudden heart attack."
Kabungo "was one of the outstanding Zambian football personalities that flew the Zambian flag at global football events," Kamanga added. "We all have to learn from his example of excellence and celebrate his legacy by breeding more hard working football Zambian administrators."
Furious Nigeria supporters stormed the pitch after rivals Ghana sealed a World Cup spot at the expense of the Super Eagles.
Arsenal's Thomas Partey opened the scoring in the 10th minute for Ghana before William Troost-Ekong levelled from the penalty spot but the hosts exited on away goals and Ghana claimed their place at the finals in Qatar later this year.
The result sparked ugly scenes inside the stadium, with videos on social media showing supporters leaving their seats and smashing equipment at the side of the pitch.
