Real Madrid began life without Cristiano Ronaldo with an extra-time defeat to bitter rivals Atlético Madrid in the Uefa Super Cup.

Quickfire goals from Saúl Ñíguez and Koke gave Atlético a 4-2 win in Estonia in Real’s first competitive match since their club record goalscorer Cristiano Ronaldo was allowed to join Juventus for £99.2m.

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Diego Costa’s two goals, either side of Karim Benzema’s header and a penalty from Sergio Ramos, ensured the match finished level after 90 minutes to force extra time at the A. Le Coq Arena in Tallinn.

With the La Liga season set to start at the weekend, playing 120 minutes in a venue located more than 2,400 miles from the Spanish capital was not ideal for either club.

Real’s new manager, Julen Lopetegui, endured a nightmare start as the European champions fell behind inside a minute to a superb individual goal from Costa. The Spain striker chased his own flick on following Diego Godín’s ball forward, held off the challenges of Ramos and Raphaël Varane and then smashed the ball past Keylor Navas at the near post from a tight angle.

Navas should have done better and he probably would not have started the match had the new £31.5m signing Thibaut Courtois, who was watching from the stands, been registered to play.

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Having not signed a replacement for Ronaldo, Lopetegui opted to select Gareth Bale in a three-pronged attack with Benzema and Marco Asensio. Bale, who scored the match-winning goals in May’s Champions League final as a substitute, created the leveller in the 27th minute. The Wales forward burst down the right past Lucas Hernández and delivered a perfect cross for Benzema to head past Jan Oblak at the far post.

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The Atlético coach, Diego Simeone, was forced to watch from the stands while serving the third match of a four-game touchline ban after insulting a match official during last season’s Europa League semi-final against Arsenal. He withdrew the World Cup winner Antoine Griezmann with 57 minutes played and saw his team fall behind six minutes later.

Juanfran, under pressure from Benzema, was penalised for handball by the Polish referee Szymon Marciniak and Ramos coolly converted the resultant spot-kick, rolling the ball into the bottom right corner and sending Oblak the wrong way.

Facebook Twitter Pinterest Atlético Madrid’s Saúl Ñíguez (not pictured) gave Real Madrid’s Keylor Navas no chance as he fired home his side’s third goal. Photograph: Maxim Shemetov/Reuters

Atlético had never previously beaten their city rivals in a final but they responded with an equaliser 11 minutes from time. Juanfran atoned for his earlier error by playing in Griezmann’s replacement Ángel Correa and the substitute cut the ball back for Costa to tap home.

Saúl put Atlético back in front eight minutes into the additional period, smashing a volley into the top right corner following a cross from the substitute Thomas Partey.

Real never conceded four goals in a match under Lopetegui’s predecessor Zinedine Zidane and were aiming to win the trophy for the third successive season. But any hopes of a fightback were extinguished in the 104th minute when midfielder Koke slotted home for the Europa League holders to give Simeone his seventh trophy as Atlético manager.