Outraged supporters flooded the field of the sold-out 60,000 capacity stadium in the capital, after Ghana upset the home team by forcing a 1-1 draw to win the African play-off on away goals and dash Nigeria's hopes of appearing in the World Cup later this year.
Some of fans smashed benches while others chanted "Pinnick must go! Pinnick must go!!", referring to the president of the Nigeria Football Federation (NFF), Amaju Pinnick.
Tuesday's match marked the first time since October 2011 that the Nigerian football team played in MKO Abiola stadium, which underwent about one-million-dollar renovation spearheaded by Africa's richest man Aliko Dangote.