Odion Ighalo's expert finish on 77 minutes, four minutes after coming off the bench was the difference between Group B favorites, Nigeria and the Swallows of Burundi.
The China-based number 9 was a surprise exclusion from Gernot Rohr's starting lineup for the Super Eagles opener but proved his worth after replacing the largely ineffective Paul Onuachu who got the nod from start.
Super Eagles had struggled to break the deadlock against a solid Burundi side who caused some problems for the Nigerian defense on the break.
With Daniel Akpeyi in goal for Nigeria(another surprise starter) having to make some top saves when called into action by the Burundi attackers.
Injury and illness had forced Gernot Rohr to shuffle his team for the opener, with Chukwueze, Paul Onuachu and Ola Aina making their tournament debut for Nigeria while Akpeyi was selected for a competitive game for the first time in 20 months.
Nigeria's best chance before the goal fell to the lively Chukwueze who blasted over the bar when Alex Iwobi found him in the box following some good footwork in the first half.
The second half saw the introduction of Ahmed Musa for captain John Mikel Obi in the 58th minute and Later Ighalo for Onuachu as Nigeria pushed on for an elusive goal.
The goal would finally come thirteen minutes from regulation time when Ola Aina's cheeky backheel found Ighalo in the box for the striker to finish superbly off the post.
Speaking after the game, Super Eagles gaffer, Gernot Rohr admitted that his team was not on their best level but attributed the underperformance to the changes he made to the team which was forced by injuries and illness.
“Our plan was to make them tired with quick passes but we missed the rhythm in the first half and in the second half it was better although we could not bring Musa and Ighalo from the beginning and [Leon] Balogun also and [Samuel] Kalu too because they were sick," the German said in his post-match conference.
“We had big problems in the preparation because half of the team had a virus with fever and then yesterday we lost two players in the last training session – Jamilu Collins and Samuel Kalu.
"Notwithstanding, the solidarity of the team was here in this difficult moment, but we have to struggle so much to win it and this is because my colleague from Burundi [Olivier Niyugenko] made a good job today."
The best chance in the first half fell to the Burundians when Cedric Amissi was played through on goal but he failed to convert when faced with Daniel Akpeyi.
Rohr agreed the first half wasn't up there for the Eagles but he was satisfied with improvements made in the second half against a difficult side.
"We could not make a better performance because the team of Burundi was very well organized, and we couldn’t have especially in the first half, the rhythm, and also I think the pressing which we had better in the second half.
"So we took a long time to come into this match and we didn’t have any opportunities in the first half because the other team was very well organized.
“We know that Burundi was unbeaten in the qualifiers and we knew also that this match, the first match will be very difficult. In our group, all the three matches will be tough matches because these teams like Burundi’s team, they don’t have anything to lose, they know us very well also, and they know how they can organize to play a defensive game against us.”