The African Champions, Super Eagles failed to pick AFCON 2015 ticket following their two-all draw with South Africa at the Akwa Ibom International Stadium on Wednesday.
Nigeria finished a disappointing third in Group A with eight points, while Congo advanced on 10 points after they won 1-0 in Sudan, with a second-half goal by Francis Nganga.
Tokelo Rantie gave South Africa the lead in the 42nd minute, when he sped past Azubuike Egwuekwe from the left flank before he fired past goalkeeper Vincent Enyeama.
Rantie scored his second goal in the 48th minute, when he sliced through the entire Nigerian defence before slotting home.
Nigeria pulled a goal back in the 68th minute through Sone Aluko after a rebound from a shot by Ike Uche, which crashed against the post.
In stoppage time, Aluko salvaged a draw for the home side with a powerful shot.
Bafana were reduced to 10 men in the 72nd minute when Reneilwe Letsholonyane was sent off.
The Super Eagles knew they had to match Congo’s result – away to Sudan – to guarantee their place at the 2015 Africa Cup of Nations, a tournament they won in 2013, incidentally in South Africa.
The Africa Cup of Nations begins next year on January 17 in Equatorial Guinea, with the final to be played on February 7.