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Madrid raced to a 2-0 lead in the first-half thanks to goals from Karim Benzema and Toni Kroos.
But Oscar Mingueza grabbed a goal in the second half to bring Barcelona back into the game.
The 84th minute saw Braithwaite chase after a Jordi Alba cross into the box and get taken to the ground by Mendy.
Braithwaite goes down and Barca are livid that the referee hasn't given a penalty
Time running out for the visitors to deny Real Madrid an #ElClasico win :eyes: pic.twitter.com/uYVUp26Lz0
- Watch ElClásico live on Premier Sports :tv: (@PremierSportsTV) April 10, 2021
:camera_with_flash: - Barcelona ask for a penalty, but it's not given. pic.twitter.com/8P33VH8vBa
- :gem: (@TheEuropeanLad) April 10, 2021
Players surrounded the referee and begged for a spot kick to be given, but none was given and there was no VAR check.
Fans have reacted to the decision and they believe it should've been a penalty and a chance at an equaliser.
Mendy literally pulled Braithwaite. Come on man.
- Lulu (@lulu_blaugrana) April 10, 2021
Mendy's tug on Braithwaite was more egregious than the foul on Vinicius that led to the Kroos goal.
- spot (@spizotfl) April 10, 2021
THATS A PEN WTF
- harshuu(pedri stan) (@fcbharshuu1) April 10, 2021
Do they even use VAR in Spainv
- Rick (@Rick08__) April 10, 2021
Benzema's opener was an audacious flick that only the world's most in-form forward could pull off.
Federico Valverde burst into the Barcelona half before laying off to Lucas Vasquez, who whipped a fierce ball towards Benzema.
The Frenchman got goalside of Ronald Araujo and caught out goalkeeper Marc-Andre ter Stegen with a flick at the near post.
Kroos made it 2-0 just past the half hour mark after his free-kick deflected in off Sergino Dest, who looked to turn away from the ball.
Mingueza bundled home in the 59th minute to give Ronald Koeman's side hope.
Casemiro was sent off for 'Los Blancos' in added time but Madrid managed to hold on for victory.
It takes them top of La Liga on 66 points for now, with Atletico Madrid travelling to Real Betis on Sunday evening.
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