Emery, hailed as a tactical genius after the demolition of the Spanish champions at the Parc des Princes, had stood proudly on the cusp of leading PSG to one of their greatest victories.
But the fall was spectacular.
PSG leaked three goals in the seven minutes allowing Barcelona an unprecedented comeback. It was the first time a side had recovered from such a huge deficit to advance.
The Catalans - roared on by nearly 100,000 fans inside the Camp Nou - played glory football with their South American troika of Lionel Messi, Neymar and Luis Suarez scoring four of the six goals. Suarez scored the opener after three minutes before a Layvin Kurzawa own goal made it 2-0 just before half-time. Roberto struck the winner at the end of stoppage time to give Barcelona 6-5.
"When you win 4-0, then lose 6-1, it's very hard to accept," said PSG president Nasser Al-Khelaifi. "Everyone knows that the quarter-finals were an objective and after winning the first leg 4-0 that aim was confirmed.
"This is a nightmare for everybody. Is Unai Emery still credible? This is not the moment to talk of this. After the game, we are all upset."
The French sports daily L'Equipe was quick to highlight the implications of becoming the shock European fall guys.
"It is the entire PSG project that is threatened by this humiliation," it said.
Emery said PSG were damaged by the decisions of the German referee Deniz Aytekin's to award two penalties to Barcelona in the second half.
Messi converted the first penalty on 50 minutes to increase hope among the partisans. But that sentiment seemed futile when Edinson Cavani scored what looked like a crucial away goal to make it 5-3 on aggregate to PSG.
But Neymar, after scoring an 88th-minute free kick to make it 4-1, scored the second penalty in the 91st minute - 5-1 - before Roberto got the vital goal in the fifth minute of injury time.
"The truth is we have let a huge opportunity get away and we are aware of that. In the first half it was more our fault than them playing well," said Spanish coach Emery.
"In the second half it changed. The Messi penalty got them off to a great start, but I was already calmer because I could see the team was responding better, were better positioned on the pitch and could do damage.
"We had chances to make it 3-2 and then the refereeing decisions, I don't know if they were right or not, but for sure they damaged us. Then in the last two minutes we lost everything we had recovered in the second-half.
"Barcelona are capable of this in their stadium. In the last few minutes they played all or nothing and they have beaten us."
PSG's defender Thomas Meunier blasted his team-mates for allowing Barcelona to bully them. "Even at 5-1 down, we were qualifying. But we conceded a goal that we should not have conceded," he said. "We acquiesced. We were victims and let them dominate us.
"Even when were 3-1 down we had lots of chances to score but we didn't take them. We made unacceptable mistakes and handed the game to them."