With Wednesday's clash at Parc des Princes played behind closed doors amid fears over the spread of coronavirus, PSG overturned a 2-1 opening-leg deficit to progress to the last eight for the first time since 2016.
Neymar got Thomas Tuchel's side started in the 28th minute, capping an impressive display with a diving header from point-blank range, before Juan Bernat doubled PSG's tally.
And with Dortmund toiling to claw their way back into proceedings, their frustrations were compounded in the closing stages – Emre Can seeing red for becoming embroiled in an off-field scuffle as Lucien Favre's side dropped out with a whimper.
With thousands of fans making their voices heard outside Parc des Princes, it was Dortmund who went close to a breakthrough against the run of play – Erling Haaland inches away from connecting with Achraf Hakimi's cross.
It was PSG's turn to rue a glorious chance in the 25th minute – Edinson Cavani racing through on goal only for Roman Burki to make a superb save with his right foot.
But Burki was beaten three minutes later, Neymar left unmarked in the six-yard box to head in from Angel Di Maria's corner.
Jadon Sancho tested Keylor Navas as Dortmund looked to respond, yet PSG turned the tie further in their favour on the stroke of half-time when Bernat diverted home.
Di Maria's long-range free-kick had Burki lunging to his right nine minutes after the restart, before Tuchel introduced Kylian Mbappe, who had been a doubt due to a throat infection.
Dortmund substitute Julian Brandt had more of an impact, though his deflected strike onto the roof of the net was the closest the visitors came to keeping themselves in the competition before Can's red card for violent conduct all but ended their slim hopes.
What does it mean? PSG end last-16 hoodoo
It has been four years since the Ligue 1 giants made it into the quarters of the Champions League, having succumbed to turnaround defeats to Barcelona and Manchester United in two of the last three campaigns.
However, now they have completed a comeback of their own, perhaps they are finally ready to launch a real onslaught on the competition.
Neymar's time finally set to come?
With Mbappe only passed fit enough to start on the bench, Neymar – who has suffered untimely injuries at this time in each of his previous two seasons at PSG – came to the fore in style on Wednesday, inspiring the French champions with his header and running the play in general for the home side.
Haaland kept under wraps
There was no doubt that, with his two goals, Haaland was the star of the first leg. However, he was nowhere near as effective this time around, with Dortmund unable to provide their front man with any service as his extraordinary run in the Champions League came to an end.
PSG will face Nice in Ligue 1 on Sunday, though of course no fans will be in attendance. Likewise, there will be no crowd at Signal Iduna Park for Saturday's Revierderby between Dortmund and Schalke.