The Welsh club came away with all three points thanks to a 3-0 victory at the Mestalla in the opening Group A fixture but it was made possible when Los Che defender Adil Rami was sent off in the 10th minute.
Rami was given his marching orders for brining down Wilfried Bony with the referee judging him to be the last man defending but Laudrup felt it was not a definite red in his opinion.
Laudrup also sympathised with Djukic after a section of Valencia fans staged an organised protest by leaving their seats at half-time before returning 10-15 minutes later.
"He will feel bad, I am a coach and I understand how he feels but these things can happen at a big club and he has to stay strong," he said.
"It was difficult with the red card because Bony is going towards goal and Rami is the last man, but there is a player coming in from the side.
"I think some referees would give a red card and others not, but he brought the red card out immediately so he had no doubt."