Roberto Martinez felt Belgium had two Nations League points taken away from them by the VAR after Brennan Johnson's late equaliser gave Wales a 1-1 draw.
Youri Tielemans' 50th-minute strike looked as though it would prove enough for Belgium, who were without Thibaut Courtois and Romelu Lukaku in Cardiff.
But Wales, who had an early Ethan Ampadu strike contentiously ruled out by the video assistant, were grateful to see Johnson's 86th-minute leveller allowed to stand despite the linesman initially flagging for offside.
Martinez, however, was left furious by the decision.
"I can't analyse this game until I get an explanation from someone about that goal against. It was a shocking decision," Martinez told VTM.
"The assistant referee makes the right decision, but somehow the VAR makes it in his head to overrule. Those lines are not parallel.
"We should have won this match. They took two points away from us tonight, it was simply offside.
"My players don't deserve this, because we defended really well."
The stalemate meant Belgium failed to capitalise on the Netherlands' 2-2 draw with Poland in the other clash in Group A4.
Martinez's side remain three points behind the Netherlands with three games played.