With the Germans trailing 2-1 in the 13th minute of stoppage time, Matthijs de Ligt thought he had equalised but the assistant referee's flag was already raised for offside.
Bayern Munich manager Thomas Tuchel says the decision from officials to stop play before his side scored an injury-time equaliser against Real Madrid "feels like a betrayal".
The Germans led 1-0 in the second leg of their Champions League semi-final up until the 88th minute when substitute Joselu scored twice in three minutes.
With Bayern trailing 2-1 in the 13th minute of stoppage time, Matthijs de Ligt thought he had equalised but the assistant referee's flag was already raised for offside.
Real defenders stopped before De Ligt fired into the net and television replays showed the original decision may not have been offside and would have needed to be checked by video assistant referee [VAR].
But having already stopped play, VAR was unable to intervene. Tuchel told TNT Sports afterwards "it was a very, very bad decision" and "against the rules".
"There was a disastrous decision from the linesman and the referee. It feels like a betrayal in the end," he added.
"The linesman says sorry but that does not help. To raise the flag in a moment like this... The referee sees we get the second ball and we get the shot.
"It's hard to swallow but that's the way it is."
Tuchel later confirmed referee Szymon Marciniak also apologised but that it "does not help" with Real in the final.
"Everyone has to go to their limit, everyone has to suffer, everyone has to play without making mistakes. So the referee has to be at that level too," said Tuchel.
"It just doesn't help to make excuses after the fact. You are on the field for this reason, because you are the best there is. And we have the right to expect that until the end."
Real will take on Borussia Dortmund in the Champions League final at Wembley Stadium on Saturday 1 June.