Real Madrid had come from behind to lead 2-1 before Ferran Torres’ 84th-minute equaliser sent the Clasico final in Seville to extra time.
Barcelona defender Jules Kounde drilled in a 22-yard screamer in the 116th minute to ultimately win a thrilling encounter on Saturday.
In the final moments, Real forward Mbappe tried to shrug off Eric Garcia and drive into the penalty area but was penalised for a foul on the Barcelona defender.
The Real bench reacted furiously, with Rudiger appearing to throw an object at De Burgos Bengoetxea, for which he was dismissed, before having to also be restrained by members of the Real coaching staff.
Vazquez, 33, was sent off for entering the field of play and protesting against the decision.
“You can see something is thrown – [Rudiger] is in big trouble, it doesn’t miss the referee by a million miles, it’s at the referee,” said Premier Sports commentator Terry Gibson.
“It’s pathetic from the Real Madrid players.”
Rudiger said the fact he had been substituted and therefore “not able to help” his team led to the “mistake” before the final whistle.
The referee report states Bellingham was later sent off for approaching the officials in an “aggressive attitude” and “having to be restrained by his team-mates”.
Video footage of the tunnel at half-time appears to show Bellingham say: “Everything goes in their favour. Every 50-50 decision goes in their favour” – though he was not sanctioned for this comment.
It is the second time Bellingham has been sent off for Real this season for dissent. He was given a two-match ban for swearing at the referee in a 1-1 La Liga draw with Osasuna in Februrary.
There were tensions between Real Madrid and De Burgos Bengoetxea in the build-up to the match.
The referee broke down in tears in a news conference over the pressure the club’s TV channel has put officials under, prompting an angry response by Real.
In February, Real Madrid wrote a formal letter of complaint to RFEF and Spain’s High Council for Sports saying Spanish refereeing was “rigged” and “completely discredited”.
After that letter, which followed a 1-0 loss to Espanyol, La Liga president Javier Tebas said Real Madrid had “lost their head”.
Later that month the RFEF condemned the “repulsive” abuse suffered by referee Jose Luis Munuera Montero for sending off Bellingham against Osasuna.
Earlier this month, Rudiger and Mbappe were given suspended one-match bans and fined for indecent conduct during their Champions League last-16 win against Atletico Madrid, with Dani Ceballos also fined.
