The Serie A side had battled back from a 3-0 loss in the first leg to pull level with the Spanish giants at the Bernabeu and the tie looked set for extra time when disaster struck for Juventus.
Medhi Benatia was adjudged to have taken down Lucas Vazquez in the penalty box as the Madrid winger attempted to get on the end of a Cristiano Ronaldo header back across the area.
Referee Michael Oliver was immediately surrounded by Juventus players, with Gianluigi Buffon sent off before the spot kick could even be taken.
Ronaldo made no mistake from the spot, and Los Blancos earned a 4-3 aggregate win to make their way into the Champions League semi-finals.
The outcome brought about plenty of anger from the Juventus side. Buffon launched an astonishing broadside on referee Oliver while Giorgio Chiellini and Juventus president Andrea Agnelli both either hinted at or flatly accused the match officials of some kind of bias.
But as it turns out their words to the media were simply a continuation of their frustrations, which came to a head in the tunnel following the match.
The confrontation saw Chiellini claiming that Madrid's players had bought the referee (as he already had said on the pitch) and other members of the team confronting the match officials and members of the Spanish side.
"The Juventus players were furious and they tried to make Real players to pay for it," a source told Goal.
Sergio Ramos, who was suspended for Wednesday's match, was in the tunnel after the clash and played peacekeeper, helping calmer heads prevail before the confrontation turned into something more.
And even with his work to try and stop a brawl between the two teams, Ramos' presence in the tunnel could cause another issue for Madrid.
Having been suspended from the match, the defender was seen watching the end of the match from the tunnel, with Spanish radio outlet COPE reporting that Oliver even noted Ramos' presence in the tunnel in his post-match report, meaning the 32-year-old could face another suspension from UEFA should they find that he was in breach of the rules concerning suspended players being on the pitch.
Xabi Alonso was handed a one-match ban for stepping on the field to celebrate with his team-mates after the 2014 Champions League final, and UEFA could take a similar view of Ramos' situation.
However, Goal understands that Real Madrid are not at all concerned about a ban for Ramos because he never actually set foot on the turf of the field, with the club believing that there is no rule stating that he can't be in the tunnel.