The Super Eagles controlled the opening exchanges but did not go on to break the deadlock until the 22nd minute. Brown Ideye managed to flick the ball on for Spartak Moscow striker Emmanuel Emenike, who in turn poked it into the net from close range.
While Nigeria continued to be the dominant force, they failed to add to their tally before the half-time whistle.
Ikechukwu Uche had a good chance to claim a second for his nation after the restart, but he shot wide from just two yards out with 65 minutes on the clock.
Despite the fact that they were at a numerical disadvantage, Nigeria still looked the more likely to score the game's second goal. However, poor finishing, particularly from John Obi Mikel, meant that they failed to find the net.
Their failure to do so was punished four minutes in stoppage time when Auxerre's Traore found himself unmarked 10 yards from goal and he responded by rolling the ball into the net.