The Nigerian senior national team were tipped to overcome the visitors but they crashed like a pack of cards.
Before the World Cup qualification game, the Super Eagles were on top of group C.
With the return match against the Les Fauves already billed for the Stade Japoma de Douala on Sunday afternoon, the Gernot Rohr side failed to get the maximum points from a team ranked about 90 places behind Nigeria in the FIFA world rankings.
The Super Eagles were lacklustre and struggled to come to terms with the pace of the game.
CAR had a goal disallowed in the first half by the centre referee.
A late strike by Karl Maxence Namnganda settled the match in favour of the visiting team.
Despite the defeat, the Super Eagles will remain at the top of group C with six points after three games while the CAR now have four points.
Meanwhile, Cape Verde stunned Liberia 2-1 in the other game of the group.