Photographs showed the fans displaying banners which read, among other things, "Respect" and "VARgogna" - a play on the Italian word "vergogna", meaning disgrace.
Flyers were handed out which listed games in which fans thought the Serie A side had been wronged.
"Fiorentina, Torino, Milan, Juve, Cagliari... not to mention those games we won in spite of incredible mistakes," the flyers read.
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Serie A is one of a number of European competitions where the VAR system is being trialled this season.
Its use was approved on a permanent basis earlier this month by soccer's rule-making body IFAB and FIFA have said it will feature at this year's World Cup in Russia.
The fans continued their protest by boycotting the start of their league match at home to Bologna, leaving the Curva Nord stand almost deserted, before entering the Stadio Olimpico in the 15th minute. There was no immediate comment from the FIGC.
(Writing by Brian Homewood in Berne; Editing by Christian Radnedge)
