Marcelo's own goal gave the European nation a surprise lead in Rio, before Neymar equalised just the before the half-hour mark with a low left-footed effort.
The host nation then took the lead when the Barcelona forward added his second of the evening from the penalty spot in the second half, before Oscar wrapped up the win late on.
However, many were left bemused when the official Yuichi Nishimura gave the spot-kick after Fred went down theatrically with his back to goal, and while Scolari acknowledged that many disagreed with the referee, he certainly wasn't one of them.
"Thousands didn't see the penalty? The referee saw it and he is the one that decides," said the Brazil boss to reporters after the game.
"We also think it was a penalty. I watched it ten times and, for me, it was a penalty."
The former Chelsea boss was fulsome in his praise of a current Blues star - Oscar - after the playmaker's telling contribution against Croatia.
He added: "Our statistics after the game show that he was the one who made the most tackles, and made lots of dribbles and crosses - he was our most creative player on the night.
"He was fantastic and that's the kind of player he is and I have always believed in him. Any doubts came from [the media]. His level may have dropped but I never lost belief in him."
Brazil face Mexico in their next Group A game on Tuesday.