Leading 1-0 from last week's first leg in France, Andrea Pirlo's stunning free-kick in the fourth minute put the Italian side in full control of the tie.
Jimmy Briand soon brought Lyon back into the contest with a classy header to silence the crowd at the Juventus Stadium, the venue for this year's final.
Juve were fortunate to go back in front in the 68th minute when Claudio Marchisio's strike took a heavy deflection off defender Samuel Umtiti past Lyon goalkeeper Anthony Lopes and hand Juve the victory.
The hosts, who had never lost at home against Ligue 1 opposition, enjoyed a strong start.
They went in front when Pirlo's curled free-kick towards the far post beat Lopes.
Lyon pressed forward and levelled matters in the 18th minute when Briand powerfully headed Arnold Mvuemba's cross past Juventus goalkeeper Gianluigi Buffon.
Lyon, looking to change a trend having lost four of their previous five European quarter-finals, gained confidence and almost went ahead before the half-hour mark.
Maxime Gonalons really tested Buffon with a powerful shot from just outside the area which the goalkeeper saved well.
Before the interval, Lyon defender Bakary Kone got to Pirlo's pass marginally ahead of Carlos Tevez to clear what could have been a good chance for Juve.
Early in the second half, Kwadwo Asamoah's goal-bound effort from outside the area was kept out by Lopes.
Juve coach Antonio Conte then brought on Spanish striker Fernando Llorente in place of Mirko Vucinic as Juve continued to push forward.
It was Lyon that came close to scoring in the 67th minute when Mvuemba forced Buffon to fully stretch to clear his powerful free-kick towards the near post.
Juve went ahead one minute later.
Lopes could do nothing as Marchisio's hard drive from outside the area took a wicked deflection off Umtiti and veered into the back of the net.
Lyon, needing two more goals to progress, could not get past Juve's defensive wall in the latter stages of the game as they bowed out of the competition.