The Stallions scored the three goals in sixteen minutes in the second half to cancel out Eswatini’s lead at the FNB Stadium in Johannesburg on Tuesday.
Striker Dango Aboubacar Ouattara was the hero for his side as he scored two goals that helped his country to the important away victory.
Sabelo Ndzinisa broke the deadlock in the 64th minute before the Burkinabes rallied to score two quick goals through Ouattara before Stephane Aziz Ki sealed the victory.
The impressive turnaround ensures that the West Africans make it two wins out of two games to open up a five points lead in Group B of the qualifiers.
Cape Verde will play Togo in the group’s other game later in the day.
Eswatini head coach Dominic Kunene made only one change to the team that came from behind to draw 2-2 with Togo in the first group game with Philani Mkhontfo replacing Peter Dlamini.
Teenager Kilian Nikiema was given his very first start in a competitive match against Eswatini in the absence of first choice goalkeeper Herve Kouakou Koffi who missed the game due family issues he had to attend.
Nikiema made his senior debut for the Stallions when he was 16 years old during an international friendly against Libya on April 4, 2019. Hassane Bande also replaced Abdoul Fessal Tapsoba in the Burkina’s line-up.
The first half of the game was barren as both sides failed to convert the few chances they created with the goalkeepers making a save each.
The hosts broke the deadlock in the 64th minute through experienced forward Sabelo Ndzinisa with his fourth goal in the last five matches for Sihlangu Semnikati.
The lead lasted for only five minutes as Ouattara got the equalising goal in the 69th minute after he was set up by Gustavo Sangare.
Ouattara scored to put Burkina Faso ahead in the 75th minute before substitute Stephane Aziz Ki made it 3-1 four minutes after coming on for Sangare.
Eswatini ended the match with ten men after defender Lindo Mkhonta was sent off six minutes from time.