The Eagles equalized in the dying minutes.
A dying minute goal by Nnamdi Oduamadi saved the Super Eagles from an embarrassing home defeat to Kenya.
The Kenyans scored in the first half as the Nigerian side found it difficult to create clear cut chances.
The first half ended with the Kenyans leading the African champions by 1-0.
The Super Eagles started the match with two players who were not at the African Cup of Nations in South Africa. Obafemi Martins returned to the attack, while Solomon Kwambe played at right back.
The Nigerian side made three substitutions in the second half with Ahmed Musa, Nnamdi Oduamadi, and John Ogu all coming in.
The Super Eagles still found it difficult to create clear cut chances as the Kenyans narrowly missed a clear-cut opportunity to extend the lead.
A dying minute goal by Oduamadi, during the 5 minutes added time after the full 90 minutes, ensured that Nigeria salvaged a point from the encounter.
The Eagles now have five points from three matches in the group, while Kenya have 2 points from three matches.