This question is based on two false premises:
- that an unintentional handball is a foul; and
- that the referee, Pitana, came to the conclusion that Perisic's handling was unintentional, yet still awarded a penalty kick.
Most free-kick offences in Law 12 (i.e. fouls) do not require intent. The majority simply require carelessness, recklessness or excessive force (i.e. charging, jumping at, kicking or attempting to kick, pushing, striking or attempting to strike, tackling or challenging, or tripping or attempting to trip). Some are simply strict liability offences - that is, the manner they are carried out in is irreleveant - all that is required is that they occurred - e.g. holding and impeding.
For handling to be an offence, it requires a deliberate act. There is no such thing as an unintentional handball foul. In Law 12 - Fouls and Misconduct, Section 1 - Direct Free Kick:
Handling the ball involves a deliberate act of a player making contact with the ball with the hand or arm.
The following must be considered:
- the movement of the hand towards the ball (not the ball towards the hand)
- the distance between the opponent and the ball (unexpected ball)
- the position of the hand does not necessarily mean that there is an offence
Using these criteria, the referee determined that Perisic moved his hand towards the ball, and therefore handled the ball deliberately. This is why the penalty kick was awarded.
I'd also like to challenge the assertion in the opening sentence of the question that referees used to ignore unintentional fouls. It is far more likely that referees were missing fouls, rather than ignoring them. Prior to the introduction of VAR, referees had a lot of difficulty getting decisions right in the penalty area at the highest levels of the game, due to quick breaks leaving them in a bad position, or players screening their vision. Now with the VAR, missed incidents are now being referred to the referee so that they can get the decision correct.