The Brazilian called referee Damir Skomina’s late penalty decision made using the video assistant referee system, a “disgrace” on social media.
Neymar, who was injured, watched United overturn a 2-0 first-leg deficit.
He will now miss half of next season’s Champions League group stage.
Neymar said the penalty, which was scored by Marcus Rashford, “doesn’t exist”.
And the 27-year-old then went on to add: “It’s a disgrace. Four guys who know nothing about football watch a slow-motion replay in front of the television.”
The referee reviewed footage of the ball striking the hand of PSG defender Presnel Kimpembe before awarding the visitors an injury-time penalty that gave them a 3-1 win in the second leg on 6 March, enabling them to progress on the away goals rule.
“What can he do with his hand while his back is turned?” asked Neymar, who missed both legs with a broken metatarsal.
Neymar returned to action after a three-month injury absence as a half-time substitute as PSG celebrated winning Ligue 1 by beating Monaco on Sunday.