Central African Republic, who are ranked 90 places below the Super Eagles, snatched the win late on in the game through Karl Namnganda. For all of their possession and chances in Lagos, Nigeria were unable to capitalise but they still sit top of Group C with six points having played three games.
The sides will meet once again in the reverse fixture on Sunday 10 October as Nigeria will search for a response to their shock defeat.
Also in World Cup Qualifying there was a win for Iran away from home against United Arab Emirates at Zabeel Stadium. Saman Ghoddos was an unused substitute for the match, which was won on 70 minutes by Mehdi Taremi.
It was almost 2-0 to Iran late on when they were awarded a penalty but the spot kick from Sardar Azmoun was saved by Ali Khaseif. Saman’s side are top of their qualifying group having claimed nine points from three matches. Next up for them is a fixture against South Korea on Tuesday 12 October.