Pitana consulted VAR when the ball connected with Ivan Perisic's hand inside the Croatia penalty area and judged that the winger had deliberately blocked it, awarding a spot-kick that was scored by Antoine Griezmann to make it 2-1 to France at that time.
Additional goals from Paul Pogba and Kylian Mbappe put the game further out of Croatia's reach before Mario Mandzukic made it 4-2 after 69 minutes and Dalic condemned the penalty decision while congratulating France.
"We played well in the first 20 minutes," the Croatia boss told reporters. "We dominated and then the penalty was given.
"I never comment on referees, but let me say one thing: in a World Cup final you don't give such a penalty, but it in no way diminished France's win.
"Don't take this as me saying something bad of the referee, I respect the referees. He did what he saw, fair and square.
"I never meant to be negative. That's how it is. With respect to VAR, when it's in your favour it's good, when it isn't its bad. That's it.
"Maybe we're a bit unlucky, maybe in other games we were favoured by luck, today we were not."
Croatia were pegged back in the 18th minute of the game when Mario Mandzukic headed a Griezmann free-kick into his own net, and Dalic said errors cost his side when it mattered.
Despite failure to deliver a victory and Croatia's first major trophy, Dalic described his players' performance against France as their best of the World Cup.
"I congratulate the players on maybe the best game we played here," he said.
"We controlled the match but conceded, and against such a strong side you can't make mistakes.
"We are sad but we must be proud also for what we've done."