Leonardo fumed that AC Milan's Europa League elimination at the hands of Olympiacos was "unjust" due to poor refereeing decisions.
Milan went to Piraeus with a three-point advantage over the Greek side in Group F, but a 3-1 defeat sent them crashing out of the competition.
Pape Abou Cisse and an own goal from Cristian Zapata put Olympiacos 2-0 up before the Colombian centre-back pulled one back for Gennaro Gattuso's team in the 72nd minute.
However, referee Benoit Bastien deemed that Ignazio Abate fouled Vasilis Torosidis when the former Roma man attempted to get his head to a corner and awarded a penalty that Kostas Fortounis tucked home eight minutes from time.
Milan sporting director Leonardo criticised Bastien's decision and lamented the fact VAR will not be used in the Europa League until next season.
"It looks to me as if the penalty was non-existent," Leonardo told Sky Sports Italia.
"On a couple of occasions too, they had this system of putting a hand on a corner as if to wait for someone else and then taking it. [Samuel] Castillejo tried it and the referee whistled to stop us.
"If you go out of the Europa League for something like that, in the days of VAR, it becomes difficult to just accept a result. It's ridiculous that a system like VAR that everyone now uses cannot be used in a European tournament.
"There was also a strange noise every time we went to attack. I don't know what it was, but it's not fair to use a sound like that to distract us every time we go forward.
"It was genuinely irritating. The referee should've stopped play and told them to stop it. After they scored, it actually got louder.
"We were three points ahead of Olympiacos, it was a difficult situation for them to win and it was in fact totally decided by these incidents.
"We know our problems and we have some players out, but I can say this was unjust."
Gattuso must now pick his players up quickly ahead of next Tuesday's crucial Serie A clash against Bologna, as they continue their pursuit of a top-four league finish.