Neymar put Brazil ahead in contentious circumstances in the 71st minute after Japanese referee Yuichi Nishimura ruled that Fred’s tumble to the floor following the slightest contact from Croatia defender Dejan Lovren warranted a penalty.
Croatia had threatened to spoil the party as Marcelo’s own goal gave them an early lead, but Neymar levelled from range before the break and Oscar then added a late third.
But it was the decision of Nishimura which dominated the post-match discussions, with Kovac adamant that his side had been harshly treated.
Kovac said afterwards: "I don't think anybody, anywhere in the stadium, saw this as a penalty.
“If you continue like this you will have 100 penalties. I think 2.5billion people watching on TV saw this was not a penalty.
"This was ridiculous and if we continue in this way we will have a circus.
"Fred is an 85kg man and I don't believe he can be brought to the ground in such a manner.
"I cannot blame Fred at all - everyone tries it on. Like it or not, this is part and parcel of football.
“What I want is for referees to stick to the laws of the game and apply them equally to both teams."
Kovac’s side more than matched their opponents, particularly in the first half, and had chances to level the match at 2-2 before Oscar’s third on the break.
The Croatia boss added: "I would like to congratulate Brazil as they are a great opponent, but I am proud of my team.
“I am a sporting person and Brazil were excellent, but I believe Croatia deserved at least a point out of this game."