Ronaldo's victor, which meant a 3-1 defeat on the night but a 4-3 aggregate victory, means Real edge one step closer to claiming a third consecutive European triumph, and fourth in five years.
Gianluigi Buffon was then sent off after referee Michael Oliver awarded Los Blancos a last-gasp penalty at the Bernabeu. If it is to be the 40-year-old's European farewell, it was a sad way to end.
Real boss Zinedine Zidane has opted to bench compatriot Karim Benzema for the clash against the Serie A leaders, with club-record signing Gareth Bale coming in for the Frenchman.
It din't take long for Max Allegri's side to silence the home crowd, after Mandzukic headed home in just the second minute.
The Bianconeri conquered the Bernabeu 3-1 and had been 30 seconds away from extra time, overturning a 3-0 first leg defeat, when Cristiano Ronaldo converted a very soft penalty. It was the first time Madrid was down 3-0 in the Champions League since losing 4-0 at Liverpool in the round of 16 in 2008-09.
GETTYCristiano Ronaldo Real Madrid want Manchester United duo Paul Pogba and David De Gea
But as the match wore on, an upset similar in scope to Roma's feats on Tuesday night against Barcelona suddenly looked a possibility, when Blaise Matuidi capitalized on a goalmouth fumble, poking home from short range to spark hope among the traveling fans.
The home defence was caught napping by Sami Khedira's run and cross, and the Croatia global had a simple header at the back post.
His second, eight minutes before half-time, was nearly a carbon copy. Stephan Lichsteiner who replaced Mattia De Sciglio early in the match delivered an excellent cross towards the Croatian whose header stunned Navas.
As the clock ticked on Juventus looked a tad lifeless but then Mandzukic popped up again with another bullet head to put his side 2-0.
In between, Real had dictated possession and created chances of their own, but Buffon was in imperious form.
Raphael Varane almost reduced the deficit on the night but his towering header crashed on the crossbar just before the halftime break.