Leading 1-0 from February’s first leg, the French side were handed a soft early penalty which Memphis Depay converted in style.
That left Juve needing to score three times to progress and Ronaldo got one back from the penalty spot.
He then thundered in his 130th Champions League goal but Lyon held on.
Lyon boss Rudi Garcia, said: “We came up against an opponent who has an extraterrestrial in its squad,” of five-time Ballon d’Or winner Ronaldo.
“This is the victory of a group. We wanted to be in the final eight in Lisbon, we are there.
“We’ll still be outsiders and that suits us very well.”
Juventus manager Maurizio Sarri may have guided his side to a ninth straight Serie A title but they were lethargic throughout and his position could be under threat.
Juve have not won the Champions League since 1996 and the wait goes on at least another year.
Uninspiring Old Lady
To question Sarri after one year in charge may seem harsh, but the reality is that in Turin – as in Paris and in Munich – winning the league is the minimum requirement.
Ending that now 25-year drought in the Champions League is the goal and were it not for Ronaldo, Juve offered next to nothing as an attacking force.
Six of Sarri’s starting XI are in their 30s and they were painfully slow in approach at times, showing why they had only actually won two of their last eight games in Serie A.
Where there is the remarkable Ronaldo there is hope, and his second on the night was a superb, swerving left-footed shot from range that gave hope of another tilt at the business end of the competition.
But when Ronaldo headed a corner over the top, that hope was extinguished.
Ronaldo could yet win the trophy with a third team, joining Clarence Seedorf in an exclusive club, but time is running out for the 35-year-old. As it may be now for Sarri, too.
“I don’t think directors of a top level will make a decision based on one match,” Sarri said after the match.
“They are going to evaluate the whole season.
“I find this kind of question [about his future] offensive, but not towards me, it’s offensive towards the directors. I have a contract, I’ll respect it and I don’t expect anything.”
Since 2003-04 (when we have the data available), Cristiano Ronaldo has scored 19 goals from outside the box in the Champions League, more than any other player
Lyon were only seventh in the French top flight when the season was cancelled in April and this was just their second game back.
They held Paris St-Germain to a 0-0 draw in the French League Cup final last Friday night – losing on penalties – and were equally resolute in Turin.
Referee Felix Zwayer helped them out with a gift of a penalty as Houssem Aouar went down after a drive into the area, with Rodrigo Bentancur clearly winning the ball.
Depay converted with a fine Panenka chip, and Lyon always looked likely to see the tie out even after Ronaldo’s double.
Depay was harshly adjudged to have handled while blocking a free-kick in the wall to give Juve a way back in and it would have been easy to cave.
But Aouar, Bruno Guimaraes and Maxence Caqueret all excelled in midfield as Lyon booked a one-off tie against City in Lisbon next Saturday night.
“It is the victory of a group. We wanted to be in Lisbon. Here we are,” said Lyon boss Rudi Garcia.
“I have been here a few times with Roma. Juventus are the best club in Italy, a team that wanted to win the Champions League and have an alien.
“We saw Ronaldo’s magnificent second goal. Few people thought we could do it. We did it.”
Man of the match – Houssem Aouar (Lyon)