Koeman’s side improved significantly after trailing 2-0 at the break at the Estadio Alfredo Di Stefano with Oscar Mingueza’s goal getting them back into the tie on the hour.
However, the Dutch boss believes his team were denied a clear chance equalise in the dying minutes by referee Gil Manzano and the VAR team.
“For me the penalty is very clear and everyone has seen it,” he told a post match interview with Marca.
“The way Martin falls, it has to be a foul. The referee may not see it, but we have a VAR for situations like this.
“However, it is better not to say more. The team has been mentally good and we deserved a decision in the penalty situation.”
The result means Barcelona slip down to third place in the table with Real Madrid leapfrogging Atletico Madrid to move top overnight.
However, Koeman knows his side need a firm reaction to this result if they want to keep pace with both of their title rivals in the weeks ahead.