In the first competitive meeting between the two sides, an own goal from Mattia Caldara and an injury time strike from Eric Maxim Choupo-Moting, gave the Parisians their first victory over Italian opposition in the competition at the seventh attempt.
As a result it is PSG who move on to the semi-finals, and became just the fourth team to win a Champions League match after being behind in the 90th minute.
For their efforts though, Atalanta equalled Lazio’s record for an Italian team reaching the quarter-finals in their debut season in the Champions League.
It looked as though it would not be the Parisians night as early as the third minute, as Neymar raced through on the Atalanta goal and, with just Marco Sportiello to beat, somehow managed to miss the target completely.
The Brazilian’s mistake appeared to give La Dea the perfect platform to control the opening 30 minutes of the game, with both controlled possession and astute tactical pressing, but created just one significant chance from Hans Hateboer.
Then came a stroke of good fortune for Atalanta, as a loose ball fell to Pasalic just inside the PSG box on 27 minutes and the 25-year-old curled a left foot effort past a helpless Keylor Navas.
Sparking the French side into life, the last 15 minutes of the first period saw Neymar flash a low drive wide, send a freekick into the hands of Sportiello, but just before the break, became the villain once more, scuffing a shot high and wide.
Rather than return with that same urgency after the break, the match settled into a similar pattern as before, with the Italians creating the odd effort and a flurry of yellow cards for both sides disrupting play.
The introduction of Kylian Mbappe brought the first significant change in Atalanta’s tactical approach, as they looked to limit the threat of the World Cup winner, but when further attacking reinforcements from the bench could not hold on.
With two minutes of normal time remaining a lofted ball into the box was played across the six-yard box by Neymar and Marquinhos stabbed the ball home off of the leg of Mattia Caldara to level the scores.
Almost directly from the restart, Mbappe was then delivered the ball in an almost identical position and free to provide the onrushing Choupo-Moting the chance to slide the ball into the net and break Atalanta hearts.
Paris Saint-Germain will now watch with interest when Atletico Madrid take on RB Leipzig tomorrow night, with the winner providing their opponent for the semi-final next Tuesday.