Following the side's elimination from European competition, the Brazil international voiced his opinions online and posted 'go f*ck yourselves' on his Instagram.
The forward, who was sidelined with injury for the match, took issue with the tie-winning penalty that was awarded in dubious circumstances.
With the tie hanging in the balance near the end of the second leg, Diogo Dalot's shot was blocked at close range by Presnel Kimpembe. And while the referee thought the VAR review was enough to award the match-winning spot-kick, Neymar took issue, posting:
"That is a disgrace! And UEFA still pick four guys who know nothing about football to review the VAR decision in slow motion... that handball simply doesn't exist!
"How do you handball behind your back? Ahh.. go f*ck yourselves."
The charge was confirmed on Friday, with a UEFA statement reading:
"Disciplinary proceedings have been opened following the UEFA Champions League Round of 16 second leg match between Paris Saint-Germain and Manchester United FC (1-3), played on 6 March in France.
"Charges against Paris Saint-Germain: Player Neymar Junior - Insulting / molesting acts against match official (statements made by the player following the above-mentioned match) - Art. 15 (1) (d) of the UEFA Disciplinary Regulations.
"The case will be dealt with by the UEFA Control, Ethics and Disciplinary Body with the date of the hearing yet to be confirmed."
Neymar has been out of action since January 23 after suffering a foot injury in PSG's 2-0 victory over Strasbough in Ligue 1.
He looks set to return in the coming weeks as the Paris club look to secure their sixth Ligue 1 title in the last seven seasons, but will now not have the opportunity to claim the Champions League trophy.
However, the forward could be forced to sit out further matches if UEFA decide to hand the him a match ban.
But, any suspension handed to the 27-year-old will have to wait until the 2019/20 campaign when PSG are back in European competition.