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Ronaldo, only introduced as a second-half substitute, was shown two quickfire yellow cards after blasting Madrid into a 2-1 lead with 10 minutes to go.
However, Real extended their advantage with 10 men thanks to a sumptuous late strike from Marco Asensio.
Earlier, Lionel Messi’s penalty had cancelled out Gerard Pique’s own goal as Barca failed to get the early season boost they needed from Neymar’s departure for Paris Saint-Germain.
The sides meet again in Madrid for the second-leg on Wednesday.
“I am proud of the players because even with 10 men they played great,” said Madrid boss Zinedine Zidane, who was hopeful Madrid could appeal Ronaldo’s red card to free him up for the second leg.
The World Player of the Year was booked for taking off his shirt in celebration after scoring and just two minutes later saw a second yellow card when referee Ricardo de Burgos Bengoetxea adjudged he had dived in attempting to win a penalty.
However, Ronaldo could be in more trouble as he pushed the referee in the back after being shown the 10th red card of his career.
“He didn’t feign anything at any moment,” protested Madrid captain Sergio Ramos.
“You have to appeal because to send off a key player with 10 minutes to go in a Clasico (the referee) had to evaluate the situation in a different way.”
– Neymar missed –
Without Neymar, Barca struggled to find their rhythm going forward as Gerard Deulofeu failed to impress in the role alongside Messi and Luis Suarez up front.
“It’s a very adverse result and we have to accept that they are the favourites now,” admitted new Barca boss Ernesto Valverde as his reign started in disappointment.
“But we need to play the second game. Everything doesn’t just come to an end after one defeat.”
The game exploded into life after the break, following an uncharacteristically quiet first 45 minutes.
Madrid immediately upped a gear at the start of the second period and were rewarded with the opening goal in a manner that would have delighted most Real fans.
Pique is often Madrid’s chief aggravator, but the Spanish international was left embarrassed as he turned Marcelo’s delivery past the helpless Ter Stegen into his own net.
Only an incredible goal line clearance from Jordi Alba then prevented Dani Carvajal from doubling Madrid’s advantage seconds later as the game began to open up.
Ronaldo had been kept in reserve by Zidane, having missed most of pre-season after his participation in the Confederations Cup with Portugal, but was finally introduced for an action-packed cameo appearance on the hour mark.
With Mateo Kovacic also replaced by Asensio, Messi was given more licence to create and led Barca back into the game as Sergio Busquets somehow blazed over from close range before Messi stung the palms of Keylor Navas.
The Argentine eventually got on the scoresheet from the penalty spot after Navas brought down Suarez inside the area 13 minutes from time.
However, Madrid took just three minutes to retake the lead in stunning fashion as Ronaldo cut inside Pique before curling into the top corner.
And with Barca pushing forward, Madrid picked the hosts off on the counter-attack when Asensio blasted into the top corner from the edge of the box as the game entered stoppage time to all but assure they will lift the Super Cup for a 10th time.
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