Roberto Martinez's Red Devils signed off from Group I in real style as Kevin De Bruyne and Christian Benteke both scored twice, albeit only after Cyprus had improbably led through Nikolas Ioannou.
The Belgian response was swift, Benteke and Yannick Carrasco scoring as De Bruyne bagged a brace before the break.
An own goal and Benteke's second following the restart saw the World Cup semi-finalists end qualifying on a remarkable total of 40 goals, more than any other side in Europe.
Hans Vanaken should have opened the scoring for Belgium after 10 minutes but incredibly missed the target from six yards following Thorgan Hazard's teasing low cross.
The hosts were swiftly punished, too, as Ioannou's left boot proved far more clinical, with a low finish sent beyond Simon Mignolet.
Belgium were behind for less than two minutes, though. Benteke failed to make contact with De Bruyne's right-wing cross but scrambled to prod in when Carrasco returned the ball from the left.
A string of Neophytos Michael saves initially kept Belgium at bay as they chased another, yet the goalkeeper gifted De Bruyne a goal 10 minutes before half-time, comically fumbling a bobbling volley into the net.
De Bruyne had his second before the break, firing in with the aid of a slight deflection, before Carrasco volleyed through Michael's legs from Hazard's centre.
It was more of the same after half-time as Michael spilled De Bruyne's shot and directed Carrasco's rebound onto the post, only to see Kypros Christoforou prod in a tame own goal moments later.
Yari Verschaeren poked a one-on-one tamely wide, but Benteke - completely out of sorts in the Premier League - was clinical when similarly sent through, dispatching the chance with his left foot.
Benteke looked destined for a hat-trick until he dallied with an open goal, allowing Christoforou to recover, with the Red Devils settling for six.