Sami Hyypia's side took the lead on the night but the Ligue 1 champions came from behind to win and confirm their place in the last eight.
Trailing 4-0 from a catastrophic first leg at the BayArena, the Bundesliga outfit was afforded no chance of progressing Wednesday, even after Sidney Sam opened the scoring with a close-range header just five minutes in.
The visitors' faint hopes were dashed soon after when defender Marquinhos registered his third goal in the competition this season to level the scores after 13 minutes - with Simon Rolfes' saved penalty signaling it was not to be for Sami Hyypia's men.
PSG has lost only once at home in all competitions since November 2012, and Ezequiel Lavezzi kept that record safe when he put the hosts in front with a cool finish from inside the area nine minutes after the break.
Leverkusen applied plenty of pressure on PSG in the second half, but the dismissal of Emre Can took away the chance to salvage pride, as the Ligue 1 champions eased into the quarter-finals.
Can had forced Salvatore Sirigu into an early stop, curling an effort on target after just three minutes, and Leverkusen's hopes of a comeback were given an early boost when Sam got on the end of Giulio Donati's cross from the right.
It was nothing more than their positive start deserved, but the hosts were level shortly after when Marquinhos rose highest in the penalty area to head home Yohan Cabaye's corner.
Zlatan Ibrahimovic, whose first-leg brace helped put Leverkusen to the sword in Germany, almost doubled the hosts' advantage with a dinked effort that struck the crossbar before captain Rolfes wasted a glorious opportunity from 12 yards to rekindle hopes of a recovery.
After Eren Derdiyok was hauled down by Christophe Jallet, Rolfes saw his penalty saved by Sirigu as the skipper spurned the chance to keep some pressure on their French opponents.
PSG then got back on the front foot before the break, Cavani swivelling well in the box before firing straight at Bernd Leno, with Lavezzi putting PSG ahead for the first time early in the second half.
Digne's cutback was met by Lavezzi, who made no mistake in tucking the ball past Leno - maintaining its impressive record at the Parc des Princes.
With nothing to play for, Leverkusen continued to play with freedom - Omer Toprak and Gonzalo Castro both testing Sirigu - while at the other end a strangely out-of-sorts Ibrahimovic ballooned an effort over the crossbar.
However, Can's second yellow card midway through the second half hampered Hyypia's side further while home boss Laurent Blanc was able to take off Lavezzi, Ibrahimovic and Cavani ahead of a tough Ligue 1 test against Saint-Etienne at the weekend.