Goals from Hans Vanaken, Leandro Trossard and Christian Benteke secured the win for Martinez, who had chosen to leave out all players with at least 50 caps, meaning the likes of Thibaut Courtois, Kevin De Bruyne, Eden Hazard and Romelu Lukaku were missing.
However, Vanaken neatly headed in a Trossard cross in the 16th minute and Trossard tapped in Belgium's second after Herve Koffi could only parry Michy Batshuayi's shot from a neat flicked lob by Adnan Januzaj.
Both sides took time to settle in the second half after multiple substitutions, until the 75th minute when Benteke won an aerial battle to head in another Trossard cross.
Burkina Faso reached the semi-finals of the Africa Cup of Nations in February, but have not qualified for the World Cup and on Thursday were thrashed 5-0 by Kosovo, ranked 109th in the world.
Against Belgium, the world's top-ranked side, they passed neatly and threatened at times, Ouattara hitting the post from distance and Nourdine Balora and Abdoul Guiebre forcing decent saves from Sels in the second half.