The Barcelona winger was lucky to escape punishment during an altercation with the Real Madrid medical staff early on in the match.
His antics were later followed by an 18th and 19th goal of the season for the Brazilian international.
Raphinha had taken exception to Kylian Mbappe receiving treatment on the pitch during the opening 45 minutes.
The Frenchman had gone down injured, with the medical staff coming onto the pitch to provide treatment.
However, Raphinha was left unimpressed before picking up a medical bag and carrying it to the sideline.
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As a result, the physios had to follow him to the edge of the pitch to continue treating Mbappe off the field.
Mbappe could be seen with strapping on his foot during the incident but was able to continue playing.
Raphinha was confronted by members of the opposition coaching team but escaped punishment from the officials.
Instead, he went on to score as Barca completed a first half turnaround in Saudi Arabia.
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Real Madrid had taken the lead after just five minutes through Mbappe before Lamine Yamal equalised.
The turnaround was then completed with two goals in three minutes from Hansi Flick's side.
Robert Lewandowski first scored from the penalty spot, with Raphinha then grabbing a third as he headed past Thibaut Courtois.
His diving header was his 28th goal contribution of the season in just 27 appearances across all competitions.
Several lengthy stoppages during the first half even left time for Barca to grab a fourth before the break.
Alejandro Balde added to Real's woes by scoring in the 10th minute of stoppage time to put them 4-1 up.
Things then got even worse for Los Blancos when Raphinha made it five after the break.
While Rodrygo grabbed a late consolation, it meant that Barcelona secured a record-extending 15th Super Cup crown.
It also meant that Barcelona have now scored at least four goals in back-to-back 'Clásicos' for the first time in history in all competitions.