However Real escaped extra-time and possibly one of the biggest upsets in Champions League history after a penalty was awarded when Mehdi Benatia fouled Lucas Vazquez in front of goal following Ronaldo's headed knock down in the third minute of stoppage time.
But Barcelona were swept aside with Roma winning 3-0 to book their place in the semi-finals of the competition.
Real's lead was completely cancelled out just before the hour mark as Blaise Matuidi capitalised on a howler from keeper Keylor Navas to cancel out the Spaniard's first leg advantage. During the game, Benatia and the rest were constantly kicking us from behind. Bayern hit the side netting through Arjen Robben before Correa saw a straight red card for a rash challenge on Javi Martinez.
97th minute: Ronaldo despatches the penalty into the top right-hand corner. He celebrated by taking off his shirt and running toward the euphoric Madrid crowd.
99th minute: Referee blows for full-time.
Diario Gol say players of the Catalan giants were wowed by the way Real refused to throw in the towel. However, they were made to work hard for their progress to the last four this time around by Sevilla.
At what was his career's last Champions League, Buffon looked visibly distraught at the so close yet so far victory.
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It was an incredible night of football that ended in a disgraceful moment.
There have been calls for Buffon to apologise for his reaction, with Oliver's wife having received vitriolic messages on social media, but Zidane felt the veteran goalkeeper simply lost his cool.
"The penalty? I don't understand why they protested, Lucas was taken down from behind".
Ronaldo admitted he had to calm himself down before stepping up and slotting home his 120th Champions League goal, followed by a shirtless celebration.
On the flip side, believe it or not, Real Madrid does have a fanbase. Just after Mandzukic got his second goal, Raphael Varane rattled the crossbar with a header to which Buffon got his fingertips.
Real Madrid had conceded two goals on the night which made the defence prone to letting in another in the second half. The Andalucian's left the Allianz Arena with a goalless draw to go out 2-1 on aggregate courtesy of their first leg home defeat.