Ronaldo had scored twice -- including his 100th goal for Real in the competition -- as they won 3-1 in the first leg in Spain last month, and his header early in the second half at the Parc des Princes effectively ended the French club's hopes of progressing.
Edinson Cavani equalised on the night for PSG, but only after they had Marco Verratti sent off, and Casemiro's late goal secured an ultimately comprehensive 5-2 aggregate victory for Zinedine Zidane's side.
PSG never looked like turning the tie around in the absence of the injured Neymar, and it was a horribly flat way for them to exit the competition.
"It was in the first leg that we lost the tie. We are all disappointed that things did not go as we hoped," Adrien Rabiot told beIN Sports.
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"We controlled the game well in the first half but couldn't get the goal to make them doubt themselves, and once we were down to 10 men it became impossible."
A year after their spectacular collapse against Barcelona in the last 16, when they were humiliated 6-1 away in the return after a stunning 4-0 win at home, PSG had hoped to produce a memorable comeback themselves this time.
Yet, shorn of the world's most expensive player, who is back in Brazil recuperating from a foot operation, they struggled to create chances, and the night will also be remembered for the stupidity of a section of their supporters.
- Di Maria flops -
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Without Neymar, this was Angel Di Maria's big chance to shine after he was left on the bench for the entirety of the first leg, but nothing came off for the Argentine against his former side, his performance symbolic of a wider malaise in the home ranks.
They had only made Real goalkeeper Keylor Navas work once in the first half, from Kylian Mbappe's shot in the 43rd minute.
That just delayed the inevitable. Having come close with a header moments earlier, Ronaldo broke the deadlock in the 51st minute, heading in a Lucas Vazquez cross for his third goal in the tie.
The goal had come from an error by Dani Alves initially, and it completely punctured PSG and the atmosphere.
The tie had escaped them before Verratti was sent off midway through the second half, picking up a second yellow card for dissent.
Unable to clear their lines in their own area, PSG saw Casemiro's shot go in via a Marquinhos deflection.
With Marco Asensio and Isco both hitting the post in the second half for Real, the visitors more than deserved their win on the night, as well as in the tie.
That rubbed more salt into the wounds for PSG, who had not lost any of their previous 51 home games in all competitions, a run going back two years to before the start of Unai Emery's reign as coach.