The Brazilian watched from the stands at the Parc des Princes on 6 March as a stoppage time penalty was awarded to Manchester United after Presnel Kimpembe was adjuged by the the video assistant referee - VAR - to have handled the ball in the penalty area.
Marcus Rashford rifled the spot kick past the PSG goalkeeper Gigi Buffon to seal a 3-1 victory and passage into the last eight.
"It's a disgrace," Neymar wrote on his social media account. "They get four guys who don't understand football to watch a slow motion replay in front of the TV ... Go f**k yourselves!"
The 27-year-old missed the match due to an injury suffered in January during a match in the Coupe de France.
Last year the 222 million euro signing from Barcelona sat out the second leg of PSG's last 16 tie against Real Madrid.
"A disciplinary investigation has been initiated ... in connection with the comments made on social media," said a Uefa statement.
If the Uefa disciplinary panel decides the Brazilian's comments are inappropriate, he faces a punishment ranging from a fine to suspension.