Marcus Rashford converted the last-gasp spot-kick to send United through on away goals after a 3-1 second-leg win in the French capital.
"It's a disgrace. They get four guys who don't understand football to watch a slow motion replay in front of the TV," Neymar, who was injured and watched the game from the stands at the Parc des Princes, wrote on Instagram.
PSG coach Thomas Tuchel said he sympathised with Neymar's frustrations.
"Sometimes you use words you take back a few hours later," said Tuchel. "You see how badly he wanted to help us."