Diego Costa’s wonderful goal after 49 seconds, the fastest goal in Super Cup history, got Atletico off to a flyer in Tallinn on Wednesday.
But Karim Benzema headed in Gareth Bale’s brilliant cross and Sergio Ramos converted a penalty awarded for a Juanfran handball to turn the tie around for Julen Lopetegui in his first game in charge of Madrid.
Despite Diego Simeone serving a touchline ban Atleti showed their fighting spirit to come from behind themselves, Costa scoring from close range before Saul’s stunning strike in the 98th minute settled a gripping contest.
The brilliant Costa then combined with Vitolo to set up Koke for a drilled fourth that gave Atletico bragging rights over their rivals as well as the first European title of the season.
Atleti took the lead in the first minute of a thrilling clash, Costa rampaging away from Ramos and Raphael Varane to slam home past Keylor Navas after chasing down his own flick-on from Diego Godin’s long ball.
Marco Asensio was close to equalising with a flicked finish from a Marcelo left-wing cross, but Jan Oblak made an excellent save.
Madrid equalised in the 27th minute, though, Bale delivering a wonderful deep cross from the right wing that Benzema nodded past Oblak.
With France forward Antoine Griezmann in muted form, Atletico gradually lost control of the contest and Madrid took the lead from the penalty spot after Juanfran handled in the area.
Ramos sent Oblak the wrong way from the penalty spot, scoring in the Super Cup for the second time and seemingly putting Madrid on course to win the trophy for the third year in a row.
But Marcelo’s mistake on the touchline allowed Juanfran and Angel Correa to combine and set up Costa to slam home an equaliser in the 79th minute.
And when substitute Thomas Partey stood up a cross from the left, Saul was on hand to lash a vicious volley into Navas’ top-left corner to regain the lead for Atletico, with Koke’s fine first-time finish in the 104th minute wrapping up the scoring.