The midfielder, whose selection was a gamble because he was still injured when the squad was submitted, came off the bench to earn his side a morale-boosting share of the points when he converted a cut back from Jonathan Pitroipa.
The stalemate followed a 1-1 draw between defending champions Zambia and Ethiopia in the earlier game at Nelspruit's Mbombela Stadium, meaning five of the six games so far at the tournament have ended in draws.
It was a cruel lesson for Nigeria who let their domination of the game slip in the closing stages after full back Efe Ambrose was sent off in the 74th minute for a second booking.
The Super Eagles paid the prize for squandering chances after Emmanuel Emenike had given them a 23rd-minute lead with a goal that demonstrated the strength of the three-man attack coach Stephen Keshi fielded.
Emenike bundled the ball home after an audacious flick on from Brown Ideye, who had three chances of his own in the opening exchanges.
Ahmed Musa's pace was also an important part of the armoury of a side Keshi is building for the 2018 World Cup.
Ike Uche came on in the second half as Nigeria sought to extend their lead and he created two good opportunities only to shoot wildly off target.
John Obi Mikel, whose Chelsea team mate Victor Moses missed the game with a hamstring injury, also ballooned a late effort wide just as Burkina Faso were beginning to stir.
Traore's entry with 25 minutes left energised his team mates and in tandem with Jonathan Pitroipa they began to worry the Nigeria defence.
The two combined four minutes into stoppage time to stun Nigeria and leave their coach in good heart.
"The confidence we have got from a point against Nigeria is going to give us heart for the games ahead," Paul Put said.