After thumping the Bundesliga side 4-0 in the first instalment, it finished 6-1 on aggregate.
PSG coach Laurent Blanc made heavy changes to his side for the game, and they eventually paid off with the hosts coming behind to secure their passage in relatively convincing style.
Although far from their brilliant best shown in the opening leg, goals from Marquinhos and a rejuvenated Ezequiel Lavezzi cancelled out Sidney Sam’s sixth-minute opener. Emre Can’s second-half sending-off only confirmed Leverkusen’s miserable exit.
However, despite PSG's victory on the night and comfortable progression over the two games, Blanc was not happy with his side's attitude.
"In the first half we began badly. My instructions were to attack and dictate the play. We were not aggressive enough, much less than I expected," he revealed after the match. "
We left too much room for this Bayer team. Consequently they broke the deadlock. It woke us up, we levelled, but if I remember the first half, Salvatore [Sirigu] kept us afloat."
"In the second half it was a little better, but tonight Paris did not deliver a memorable performance. It's hard to tell your team to ignore the result of the first leg – it's complicated. We always had this in our minds, that we still had this four-goal lead."
"A Champions League game is still a game at a very, very high level. Today it was not a great performance from us, but we were powerful enough to win the match."
In reaching the Champions League quarterfinals, Blanc has now equalled Carlo Ancelotti’s performance from last season. The Parisians will feel confident whoever they are drawn against in the last eight, but also must realise that they will not have it as easy as they did over the past two legs.
For Leverkusen though, their humiliation is over. Although they were much improved at the Parc des Princes from their drubbing three weeks previously, they still lacked the necessary quality to progress.
Here are six things we learned from PSG’s 2-1 win on the night and 6-1 aggregate triumph.