Kevin de Bruyne scored twice for the hosts, who surprisingly fell behind to Nicholas Ioannou’s fine strike.
Christian Benteke levelled with the first of his two goals, as Yannick Carrasco and an own goal by Kypros Christoforou added to the scoring.
Roberto Martinez’s side finish top of Group I after scoring 40 goals and winning all 10 of their matches.
Belgium, who have never lost to Cyrpus, have now won 14 of their 16 matches since finishing third at the World Cup finals in Russia in 2018.
Despite being stunned when Ioannou scored a superb individual goal, for much of the match Belgium looked irresistible as they swept forward at every opportunity.
De Bruyne, Eden Hazard and Carrasco all came to the fore, while Benteke, who recently ended his international goal drought against San Marino, could on another occasion have registered at least a hat-trick.
The only slight concern for Martinez will have been the ease with which Ioannou raced through to score, with Jan Vertonghen’s absence from the backline clearly felt.
However, while Cyprus became only the second team to score against Belgium in the group, Martinez’s side go into next summer’s tournament with the joint best defensive record of any qualifying nation after conceding just three goals.
