Two excellent late goals from Koke and Saul sealed victory for Atletico after the game ended 2-2 in normal time.
It was Real’s first match since Ronaldo signed for Juventus for £99m in the summer and Zidane was replaced as manager by former Spain coach Julen Lopetegui.
Koke’s smart finish and Saul’s sensational 16-yard volley in extra time helped Europa League holders Atletico win their third Super Cup in as many appearances.
Diego Costa also scored twice in normal time, thumping in the opener after 49 seconds and tapping in another after the interval.
Gareth Bale had set up Karim Benzema with a header at the back post for Real’s first and captain Sergio Ramos slotted home a penalty for a 2-1 lead after Juanfran was penalised for handball.
Full-back Marcelo squandered an excellent chance to score the winner for Real with an overhead kick in the final seconds of normal time as back-to-back Champions League winners Real were looking to become the first side to win three Super Cups in successive seasons.
It was the fourth time in the past five years that the Super Cup was contested by two Spanish sides – but the first with both teams from the same city.
While Real Madrid are adjusting to life without Ronaldo, it was Atletico who provided the late heroics familiarly associated with their recently departed striker.
The club’s failure to sign a direct replacement as of yet will remain a concern for fans following this defeat but there was still plenty of encouragement in Real’s remaining attacking options.
Marco Asensio and Bale are two players who will hope to benefit from Ronaldo’s exit and both started on opposite flanks, often switching and cutting inside to link-up with Benzema.
Bale’s pace and pinpoint cross from the right teed up Benzema’s equalising goal and the Welshman’s fizzing strike had Jan Oblak scrambling in the first half
Asensio came close to scoring too when his audacious flick was superbly parried by the Slovenian keeper before a bending effort bounced wide of the right post. And Benzema seemed to embrace taking a lead role in the centre of attack – his goal capping off a strong performance.