De Ligt scored deep into stoppage time for what would have been a 2-2 goal that likely would have sent the match into extra time at the Santiago Bernabeu Stadium on Wednesday (Thursday AEST).
But the goal didn't count because the referee blew the whistle for offside without letting the play be completed.
"The linesman said to me, 'I'm sorry, I made a mistake'," De Ligt said after the 2-1 loss in which Madrid's stoppage-time winner by Joselu came after a VAR intervention that overturned an initial offside call. On that occasion, though, the other linesman allowed the play to continue.
"The rule says that if it's not clear offside ... you have to keep playing," De Ligt said.
"And if you go in the last minute and you whistle like this, I think this is a big mistake. If it's offside or not, I don't know, VAR can check it, but if you don't check it, how can you see it? This is a shame."
The VAR also came into play in the 71st minute to disallow a Madrid goal because of a foul by defender Nacho Fernandez on Joshua Kimmich.
The victory sent Madrid into the final against Borussia Dortmund on June 1 in London.
Madrid coach Carlo Ancelotti said his defenders stopped after the whistle was blown before the De Ligt goal.
"The last play is clear, the referee blows the whistle and we stop," he said.
"This referee is very good, he refereed in a World Cup final. They complain about this and we complain about the goal by Nacho that was disallowed. Kimmich threw himself to the ground."
The match referee was Szymon Marciniak, who officiated the 2022 World Cup final between Argentina and France in Qatar.
Bayern coach Thomas Tuchel said it was a "disastrous decision from the linesman and from the referee".
"It feels almost like a betrayal in the end because of that decision," he said. "The linesman said sorry. That does not help.
"To raise the flag in a decision like this, in a close decision in the last minute, and the referee as well ... the referee does not have to whistle.
"He sees that we win the second ball, he sees that we get the shot away. To whistle is a very very bad decision. It's against the rules and it's a bad decision from both of them."
