This was despite the fact that they played for half the game with an extra man at the Vicente Calderon.
Gokdeniz Karadeniz gave the visitors a dream start when he netted after five minutes and then a moment of madness by Atletico goalkeeper Sergio Asenjo gifted Pablo Orbaiz a second goal in stoppage time as Rubin claimed a potentially decisive advantage.
Atletico began the game brightly but it was the visitors who struck first.
Former Malaga striker Salomon Rondon found himself in space after receiving a first-time pass to shoot just inside the area. Atletico's second-choice goalkeeper Asenjo could only parry the shot and Karadeniz lapped up the rebound to silence the Calderon.
Atletico's attempts to find an equaliser barely troubled the visitors, and it was Rubin themselves that created Atletico's first dangerous opportunity, as captain Roman Sharonov headed a cross from Tiago towards his own goal but goalkeeper Sergei Ryzhikov saved his blushes.
Rubin soaked up the pressure and nearly scored with their second attempt, with Rondon finding himself one-on-one with Asenjo after taking down a long ball, but this time the Atletico keeper stood his ground to deny the Venezuelan.
With a minute to go before half-time Atletico were given a major boost when Sharonov was sent off for a second bookable offence. And the Primera Division high-flyers almost equalised from the resulting free-kick, with Arda Turan squaring the ball to Filipe Luis, who put his shot just over the bar.
But even with a man advantage Atletico were unable to get back into the game.
Rubin were more than happy to sit on their lead and remain in their own half, and they proved very difficult to break down.
Atletico's best attempts came from headers and efforts from distance. Felipe Luis headed over from the penalty spot, Tiago's header was saved on the line by Ryzhikov and then Adrian Lopez glanced a Raul Garcia cross wide from inches out.
Arda and Cristian Rodriguez also saw their long-range efforts tipped away by an on-form Ryzhikov, and Falcao hammered the bar from outside the area.
Atletico were searching for an equaliser right until the end, so much that Asenjo went up into the opposing box to contest a corner in injury time.
It was an inexplicable decision and Rubin cleared the corner and launched a quick counter-attack, ending with former Athletic Bilbao midfielder Orbaiz racing through the middle, beating a scrambling Asenjo to pass into an empty net.
Atletico beat Athletic Bilbao in the final to win this competition last year, but it was a former Athletic player that has made their task of picking the trophy up again in May even harder.