The Brazilian, who was among PSG's top performers on the day, received a yellow card in stoppage time while waiting to take a free kick.
While waiting to take the free kick, Neymar motioned to Kuipers to indicate that Napoli players were not the proper distance away.
The PSG winger was issued a yellow card soon after for arguing with the official, and Neymar responded with a sarcastic applause to the incident.
PSG were unable to score in the aftermath as the club settled for a point, and Neymar was less than thrilled after the match.
"The referee told me something he shouldn't and it was disrespectful," he said following the draw.
Napoli's equalizer came on a controversial penalty as Jose Callejon appeared to be offside on the lead-up to the incident.
Lorenzo Insigne buried the subsequent spot kick, canceling out Juan Bernat's first half finish as both sides settled for a point apiece.
“The Napoli penalty came from a situation that was offside in the build-up," PSG boss Thomas Tuchel said after the match.
"Plus we should’ve had a penalty and the result certainly could’ve been different with those decisions.
“Having said that, we have to accept the result and move on.”
Napoli and Liverpool sit level on six points at the top of the group.