Atletico took the lead after just 49 seconds in Tallinn courtesy of a fine solo effort from Diego Costa, but a Karim Benzema header and Sergio Ramos penalty saw Real turn the game around by just after the hour mark.
Costa doubled his personally tally 11 minutes from time to force extra time, though, and a stunning volley from Saul Niguez saw Atletico regain the lead before Koke wrapped up the win six minutes later.
Find out how all of the action unfolded in Julen Lopetegui's first match in charge of Real courtesy of Sports Mole's minute-by-minute updates below.
That is not the only first tonight, though; this will be the first European club final played in Estonia, it is the first time in this competition's 43-year history that two clubs from the same city have contested the final, and it is the first match of the post-Cristiano Ronaldo and Zinedine Zidane era for Real Madrid.
It is a match worthy of the Champions League final - indeed it has graced that stage twice in the past five years - so let's waste no time in getting started with the team news...
Well, the headline news is that there is no Thibaut Courtois for Real Madrid tonight, with an apparent admin error scuppering the Belgian's chances of making his debut against his former club.
Courtois completed his £35m move from Chelsea almost a week ago now, but reports broke earlier today suggesting that Madrid had failed to register him with UEFA in time, meaning that Keylor Navas is named between the sticks. Courtois, meanwhile, will have to wait until Saturday for his debut.
Modric's participation in the World Cup - where he won the Golden Ball having helped Croatia to the final - could be part of the reason behind that, although Varane also played in that game and starts this evening.
Benzema endured a hugely disappointing 2017-18 season, scoring just five league goals, while Asensio and Bale will hope for more regular starts under Lopetegui. Bale in particular appears to have been promised a very prominent role in the team, and tonight he makes his first competitive since coming off the bench to score twice in the Champions League final against Liverpool.
The likes of Ramos, Marcelo and Kroos all feature from the off despite the league season beginning this weekend, while in reserve Los Blancos notably have 18-year-old Vinicius Junior, who has now completed his big-money move from Flamengo.
There is also a debut for Rodrigo in midfield, and plenty of scope for more as the game goes on with Arias, Gelson Martins and Kalinic all among the substitutes.
Costa is perhaps the one striker in world football who could match Ramos's level of skullduggery so that should be an interesting battle, while Griezmann's decision to stay at the club rather than joining Barcelona could prove to be the best piece of business Atletico do all summer.
Gimenez, Luis, Partey and Correa are the men to make way for that quartet, although all of them are included on the bench alongside free signing Gelson Martins.
Simeone's behaviour during his side's semi-final victory over Arsenal earned him a four-game touchline ban in European competition, and this will be number three having also missed the Europa League final.
Los Blancos have only won the trophy four times in total in the past, and three of those have come in the last four finals - in 2014, 2016 and 2017. Another victory tonight would see them join Barcelona and AC Milan as the most successful teams in UEFA Super Cup history with five titles.
This is one trophy that Madrid will have to win without their former talisman Cristiano Ronaldo, though, with the five-time Ballon d'Or winner having moved to Juventus earlier this summer. It is impossible to replace a player like Ronaldo - aside from bringing in Lionel Messi - so it will be very interesting to see how the European champions fare without the man who scored 450 goals in just 438 appearances for the club.
It is never easy to lose arguably your greatest ever player - and the fact that he is even in the debate alongside the likes of Di Stefano, Puskas and co is a mark of his achievements - but to also lose your manager and another of the biggest figures in the club's illustrious history is difficult for anyone - even Real Madrid - to cope with in one summer.
The Frenchman stepped down just days after the victory over Liverpool - taking the football world by surprise in the meantime - and Lopetegui certainly has big shoes to fill. Zidane is now one of only three managers to have ever won the Champions League three times, joining Bob Paisley and Carlo Ancelotti in that exclusive club.
Lopetegui had been due to lead Spain in the World Cup this summer, but he agreed terms with Madrid without telling the Spanish FA until the last minute, forcing them to take drastic measures and sack their unbeaten boss on the eve of the tournament.
Indeed, Los Blancos not only finished a whopping 17 points adrift of champions Barcelona, but they also finished behind tonight's opponents, conceding 44 goals, which was their highest tally since 2008-09.
Los Blancos will resume league duties again this weekend, with a home tie against Getafe - who impressed en route to an eighth-placed finish last term - first up for them on Sunday.
Diego Simeone's side will also take on Rayo Vallecano, Celta Vigo, Eibar and Getafe in their first five league outings, with their first top-three clash not coming until the Madrid derby on September 29, and their first meeting with champions Barcelona coming on November 24.
Even so, coming three points above their city rivals Real makes for a successful campaign, and it was only their second top-two finish in their last 22 seasons, following on from their title win in 2013-14.
The bigger problem comes at the other end, where they were the lowest scorers in the top four. Despite the presence of Griezmann and Costa, Atletico still scored 41 goals fewer than champions Barcelona.
Crashing out of the Champions League in the group stages was, of course, disappointing for the capital outfit, but they made the most of it by going all the way in the Europa League, beating Arsenal in the semi-finals and then cruising to a 3-0 triumph over Marseille in the final.
It was the club's third Europa League crown in the past eight years, during which time they have also reached two Champions League finals - both of which ended in defeat to tonight's opponents.
Victory tonight would see them become the first club to make it three wins from three in the competition, while they are currently level with Anderlecht, Juventus and Valencia on two wins and zero defeats.
Atletico lost to PSG and Inter Milan in their two subsequent ICC outings, while they have also drawn with Stuttgart and scraped past Cagliari.
Whichever part of Madrid the trophy goes to, it will be Spain's 15th triumph overall, streaking further clear of Italy (9) and England (7) as the most successful country.
Both teams have named strong starting lineups for this one, and it is likely to be a tight affair. Atletico seem to have Real's number domestically and, while this is a European clash, it is not the Champions League, which is a tournament Real really seem to turn it on for.
I'm predicting a losing start for Lopetegui!
SPORTS MOLE SAYS: Real Madrid 0-1 Atletico Madrid
Real Madrid have only won one of their last 10 La Liga Madrid derbies, but they have beaten them in the Champions League in 2014, 2015, 2016 and 2017. Can they add 2018 to that list via the extension of the Super Cup?
Atletico have won two of those nine games, but never a knockout tie, with Real registering five wins in that time.
The reverse fixture back in November ended in a goalless draw, meanwhile.
REAL MADRID STARTING XI: Navas; Carvajal, Varane, Ramos, Marcelo; Kroos, Casemiro, Isco; Bale, Benzema, Asensio
ATLETICO MADRID STARTING XI: Oblak; Juanfran, Savic, Godin, Hernandez; Saul, Koke, Rodrigo, Lemar; Costa, Griezmann
It is brilliant play from the former Chelsea man too; he flicks the ball on to himself and shrugs off a challenge from Ramos, who should have done a lot better. Costa then powers past Varane and smashes the ball inside the near post from the tightest of angles.
It did not look possible to score from there, but he hit it with such venom and accuracy that not too much blame can even be attributed to Navas at the near post.
Diego Costa scores after 51 seconds, the fastest goal in history of the European Super Cup! #Supercup2018— Gracenote Live (@GracenoteLive) August 15, 2018
What a start, what a goal!— Football on BT Sport (@btsportfootball) August 15, 2018
Costa fires Atletico ahead inside a minute 🔥 pic.twitter.com/8y3SaZFTAX
This goal is all about Bale, though; the winger bursts past one defender with pure pace down the right flank and then swing a beauty of a cross into the middle with his weaker foot. Oblak cannot come for it while the defender's can't intercept it, leaving Benzema there to just nod it home from close range.
I'm not sure whether Oblak would have reached that if it was on target!
Ronaldo gone, no worries...— Football on BT Sport (@btsportfootball) August 15, 2018
What an assist from Gareth Bale 🔥
Pure pace! pic.twitter.com/FZQWcolUwe
HAHAHAHAHAHHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHA pic.twitter.com/t4ea7uuBqT— M•A•J¹³ (@Ultra_Suristic) August 15, 2018
It has been an entertaining affair so far, with Real dominating possession as expected by Atletico proving as tough to break down as ever. A very interesting 45 minutes awaits!
There were a number of defensive errors from Real, with Ramos being shrugged off too easily and Varane not making a challenge. Take nothing away from Costa, though, his finish and the build-up to it was the former Chelsea striker at his very best.
Bale burst past one defender before swinging a beauty of a cross to the back post, where Benzema had peeled away from his marker to nod home. While there were plenty of errors from Real's defence for the opener, there was not a great deal Atletico could do about the equaliser due to the quality of the cross.
It is Real who have looked more like getting a second goal, with Asensio's flick drawing a smart save from Oblak, but they have largely been limited to long-range efforts.
Ramos strolls up to the spot kick, watches the keeper all the way and then sends him the wrong way, tucking his effort into the bottom corner. Real lead!
It is really poor from Marcelo as he keeps the ball in play but only succeeds in playing Juanfran in down the right. Juanfran in turn squeezes a pass inside for Correa, who reaches the byline inside the area before cutting in back into the six-yard box, where Costa is waiting to fire into the roof of the net from close range!
Diego Costa got both goals for Atletico, while Benzema and Ramos are on the scoresheet for Real.
The chance initially looks like it might have gone when Costa's pass to Partey is a little overhit, but the winger manages to send it back into the middle for an unmarked Saul. The midfielder still has plenty to do, though, and he catches his volley brilliantly to leave Navas with no chance.
Oh. My. Word.— Football on BT Sport (@btsportfootball) August 15, 2018
We could make a "Better call Saúl" pun but we won't.
That goal was 💥🔥 pic.twitter.com/OVYPq2dnZ6
Costa turns the ball back to Vitolo, who in turn sweeps it into the path of an unmarked Koke. The midfielder still has work to do to finish it, but his first-time effort leaves Navas no chance and it nestles into the bottom corner.
Simeone's side now lead 4-2 over Real Madrid courtesy of goals from Saul and Koke, both of which were of real quality. Real have just 15 minutes remaining to get back into this game now!
Real Madrid concede (at least) 4 goals in a single match for the first time since 21 November 2015, when Real lost 4-0 at home against Barcelona in La Liga. #SuperCup— Gracenote Live (@GracenoteLive) August 15, 2018
Two goals from Diego Costa either side of strikes from Benzema and Ramos sent the game into extra time, but Atletico pulled away in the opening 15 minutes of the additional period with Saul Niguez and Koke getting the goals which ultimately earned Atletico the trophy.
It is not a good start to life at Madrid for Lopetegui, and there are questions to be answered regarding how they will cope without Ronaldo now.
Thank you very much for joining Sports Mole for tonight's match as Atletico Madrid beat city rivals Real in extra time to win the 2018 UEFA Super Cup in Tallinn. I will leave you with our match report, and be sure to check back in at the weekend when the Spanish domestic season gets underway!
From me, though, it is goodbye for now!