The French champions won 2-0 away at Manchester United in the first leg and although they were 2-1 down on the night they were going through on aggregate until the stoppage time penalty award gave United a shock 3-1 win.
Injured Paris St Germain striker Neymar lashed out at the video assistant referee (VAR) system on Wednesday, calling the late penalty decision that led to their elimination from the Champions League a "disgrace".
The French champions won 2-0 away at Manchester United in the first leg and although they were 2-1 down on the night they were going through on aggregate until the stoppage-time penalty award gave United a shock 3-1 win.
The spot-kick, awarded for handball against Presnel Kimpembe after the referee consulted the VAR, put the English club through on away goals.
The decision infuriated Neymar, who watched the match from the stands after returning a few hours earlier from partying at Rio de Janeiro's famous carnival.
"This is a disgrace!! And they put four guys there who don't understand football to look at a slow-motion replay ... It's just not possible!!!"
"How is a guy going to hold his hand behind his back," he wrote in Portuguese on Instagram, before finishing with an expletive commonly used in Brazil.
Neymar missed both legs of the tie after injuring his foot in January.
PSG manager Thomas Tuchel said he understood Neymar's anger at the decision and defended his comments, saying they were made in the heat of the moment.
"Of course it's a strong reaction, he was at the field. Sometimes when you remember yourself in a big fight and you remember being very emotional, you use words and you react in a way that you take back some hours later," Tuchel told reporters.
"He wanted to come back with us in the quarter-finals and he's been biting his nails at every game we've played without him, so don't be too harsh on him.
"I wouldn't over-interpret the use of his words. In the heat of the moment, it's quickly typed into a smartphone."
The Brazil captain joined the French club from Barcelona in August 2017 for a world record fee and the Champions League has become the holy grail for him and a club that have spent big to fulfil that goal.
However, this latest defeat marked the third time in three years they have failed to make the last eight of the Champions League.
Even though Wednesday's loss was just their third in 51 European games at the Parc des Princes, they have never reached the semi-finals of the continent's premier club competition since being taken over by Qatar Sports Investments in 2011.