Leading 4-0 from the first leg in Germany, it would have taken a huge upset for PSG not to progress and, despite having a couple of scares, the big-spending French champions did just that with a second-leg triumph at the Parc des Princes.
The first scare for Laurent Blanc's men came when Leverkusen took the lead after just six minutes through Sidney Sam, but the hosts quickly responded with Marquinhos heading them level just seven minutes later.
PSG nerves would have been tingling again just before the half-hour when battling Leverkusen won a penalty.
A goal then could have made things interesting, even though Leverkusen would still have had a massive mountain to climb - but Simon Rolfes saw his spot-kick saved by Salvatore Sirigu and PSG did not look back after that.
Ezequiel Lavezzi put them 2-1 ahead on the night at the start of the second half before Leverkusen lost Emre Can to a red card, ending any slim hopes of a possible upset.
History was against Leverkusen with only two clubs ever having won a tie in the competition after losing at home in the first leg, while Sami Hyypia's men were also without a win in their previous six matches, losing five.
However, the 2002 Champions League finalists were determined not to go down without a fight and they stunned PSG when Sam gave them an early lead, the Germany international getting on the end of Giulio Donati's cross to head home at the far post.
PSG, who are still in contention for three trophies in the next few months, did not take long to hit back though, with star man Zlatan Ibrahimovic almost inevitably involved.
He was unlucky not to net the equaliser himself, Leverkusen goalkeeper Bernd Leno deflecting his low shot behind with his leg, but from the resulting corner PSG did score with Marquinhos powerfully heading in Yohan Cabaye's flag kick.
Ibrahimovic then came within inches of putting PSG ahead in the 18th minute when his dink over Leno came back off the crossbar.
PSG seemed to have recovered from that early setback, but they received further warning Leverkusen were not going to roll over as the visitors won a penalty in the 27th minute when Christophe Jallet tugged back Eren Derdiyok.
That was a great chance for Leverkusen to put the pressure on PSG, but Sirigu dived to his left to push away Rolfes' spot-kick.
PSG made sure the escape was not wasted.
Leno denied Edinson Cavani before the break but he was powerless to stop Lavezzi slotting in Lucas Digne's cut-back in the 53rd minute, the ball going through a group of players on its way into the net to make it 2-1.
Still Leverkusen refused to concede the fight, and Sirigu needed to produce a brilliant save to keep out Gonzalo Castro's shot two minutes later.
The visitors' hopes of at least avoiding defeat on the night suffered a major blow in the 68th minute, though, when Can was shown a second yellow card for diving.
Both sides continued to create chances, Derdiyok and PSG duo Javier Pastore and Adrien Rabiot being denied by the respective keepers, but there was never any doubt who was going through.