With the score locked at 1-1 in Sao Paulo, referee Yuichi Nishimura pointed to the spot as Dejan Lovren was adjudged to have brought Fred down in the 69th minute.
Replays indicated Lovren only brushed his opponent's arm, with Fred falling dramatically, and Nishimura awarded the spot-kick, which Neymar converted to complete a brace and give Brazil the lead.
Scolari said he believes it was a foul inside the area.
"For me it was a penalty, there are things that everyone interprets differently. It is the interpretation of the referee," Scolari said.
"I have seen it repeated 10 times on TV."
Scolari heaped praise on midfielder Oscar, who laid off the pass for Neymar's long-range equaliser before scoring the sealing goal himself late-on with an opportunistic effort.
"He was the player who stole balls and created chances," the Brazil coach said.
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