Thirteen years after Roy Hodgson saw his Inter Milan side lose the UEFA Cup final to Schalke after an agonising penalty shootout, it was European heartache again as a double salvo from Diego Forlan sunk his battling Fulham side and handed Atletico the inaugural Europa League trophy.
It was a performance of undeniable bravery and guts from a Fulham team playing their 63rd game of a gruelling season, but Forlan was the difference - just as he was in the semi-final against Liverpool - showing the anticipation and predatory instinct that have characterised his game since his move to La Liga from Manchester United.
In the 2001-02 Champions League semi-final, Forlan was brought on by United boss Sir Alex Ferguson to find the decisive goal when the second leg against Bayer Leverkusen was poised on a knife edge. On that night he was profligate, on this he was prolific.
If Forlan had any demons left to exorcise from his ill-fated spell at United, they were well and truly banished as he fired Atletico to their first major European trophy since the 1962 Cup Winners' Cup and cemented his status as a cult hero at the Vicente Calderon.
But Forlan must not hog all the credit, as this Europa League triumph marks a huge turnaround in fortunes for Atletico, and that revolution has been led by boss Quique Sanchez Flores. While much of the pre-match discussion had centred around English manager of the year Hodgson, and the possibility of him emulating the great Bobby Robson, it is Flores who will now rightly receive all the plaudits.
When Atletico sacked Abel Resino in October, they were 15th in the Primera Division and were bottom of their Champions League group having failed to score a goal. Flores injected immediate confidence into his team after being handed the reins and that Atletico now stand ninth in the league and on the verge of winning a double - they play Sevilla in the Copa del Rey final next week - is a tremendous testament to his motivational skills.
When Flores took charge, strike partners Sergio Aguero and Forlan looked like strangers but he has helped lift the duo and they combined well on a number of occasions against Fulham, though their chances were limited by a Cottagers defence that defended resolutely throughout.
In truth, it was a magnificent defensive display from Hodgson's back four. Brede Hangeland, Chris Baird, Aaron Hughes and Paul Konchesky consistently thwarted Atletico's attacks, and not for the first time this season, the black and white sponge soaked up pressure, but looked dangerous on the counter-attack.
There were question marks about the fitness of Bobby Zamora, and he started the game with a heavily strapped ankle and pumped full of painkillers. He was as usual an effective outlet and it was his powerful run that helped open up the Atletico defence for Simon Davies' equaliser, coming just five minutes after Forlan's first.
Fulham had come out of the blocks looking like a team determined to prove themselves on what was for most of their players the biggest stage of their careers. Some expansive passing football was interspersed with the old failsafe of knocking it long to Zamora, with Duff and Gera the creative influence.
There were however a couple of nervy moments when the ball was given away by Etuhu and Murphy - who did his best impression of former Liverpool team-mate Steven Gerrard with a wayward pass towards his own goal that was nearly punished by Forlan but for the post. Just a few minutes later and the Cottagers weren't so lucky as Forlan pounced, though Davies would level things up.
Spurred on by the incessant noise of their supporters, belting out chorus after chorus of "stand up if you still believe", Fulham battled through the second half and into extra-time, with fatigue becoming more evident by the minute.
Aside from a save in the first half and a crucial interception from Forlan's cross in the second, Mark Schwarzer was untested, and there was to be no repeat of the four-goal trauma of the UEFA Cup final defeat suffered by Middlesbrough at the hands of Sevilla in Eindhoven in 2006, as Atletico seemed determined to give the crowd behind the goal some catching practice.
But just as the Cottagers looked to be hanging on for the lottery of penalties, Forlan was on hand again, darting to the near post in the 116th minute and turning the ball past Schwarzer, via a deflection off the colossal Hangeland.
Atletico's success means Forlan will no longer be haunted by ghosts of European competition past and Flores can continue to build a team high in ability and confidence. The Rojiblancos may not have been at their best, and they may have won just three matches on their way to their Europa League triumph, but they will surely be the only team from Madrid boasting any silverware at the end of this season.
MAN OF THE MATCH: Diego Forlan. The award was heading to Brede Hageland who was an immovable object at the back for Fulham, but Forlan was in the right place at the right time to steal all the headlines. Serigo Aguero showed flashes of brilliance at times but it was the finishing prowess of his Uruguayan strike partner that won the match for Atletico.
ATLETICO VERDICT: They often made it look difficult and were far from their best against a side with a fraction of their budget and without the plethora of star names that ply their trade at the Vicente Calderon. But Atletico did generally use the ball better and continued to attack throughout, showing a great deal of patience when they could have been frustrated. In the end it was the quality and comparative freshness of Atletico's players that helped them to triumph.
FULHAM VERDICT: Fourteen years ago, as Hodgson prepared to become Inter Milan boss, Fulham finished 17th in the bottom tier of the English football league. Their ascent from that position has been remarkable and the players and the manager must be given the full credit they deserve. They can certainly build on their success this season, having proved they could mix it with the big boys throughout their run to the final. This time, however, it was just one game too far.