Diego Simeone's men face an uphill task to stay in the Europa League as they go down to strikes from Gokdeniz Karadeniz and Pablo Orbaiz.
Kurban Berdyev's men struck early through Gokdeniz Karadeniz in the first 10 minutes, and rode their luck for the majority of the match after the first half dismissal of captain Roman Sharonov. However, the Russian side ultimately held out and netted again in the dying minutes through Pablo Orbaiz when Atletico was committing heavily for the equalizer.
The visiting outfit got off to the perfect start and netted the opening goal with just six minutes on the clock. Karadeniz cut in from the left side and slid the ball into the feet of Salomon Rondon, who drilled a shot towards the bottom corner. Sergio Asenjo in the Atletico goal managed to palm the ball to his right, but Kardeniz ran in to smash the rebound into the corner with a composed finish.
Los Colchoneros almost made an immediate reply. Arda Turan curled an out-swinging corner kick to the edge of the area for Diego Godin, but the Uruguayan's impressive volley fizzed past the post.
Rubin was dealt a blow just before the break. Sharonov, who had previously been booked for a foul on Cristian Rodriguez, was shown a second yellow card when he tripped up Radamel Falcao as the Atletico man was jinking his way into the penalty area.
The home side looked bright after the break, with the man advantage proving to be telling in the middle of the park.
Atletico should have equalized a quarter-hour into the half when Arda whipped in a teasing delivery to the front post and Tiago rose high to power a header towards goal. Luckily for Rubin, the attempt was straight down the throat of goalkeeper, Sergei Ryzhikov.
As the second half progressed, Diego Simeone's men turned up the heat, but the in-form Ryzhikov was proving to be a formidable barrier between the sticks.
In quick succession, the Rubin 'keeper denied Arda's strike from the edge of the box with an unconventional save with his legs, and managed to block a volley from Falcao from the same position.
Things just did not seem to be coming off for the Colombian on the night. With 12 minutes remaining, he turned swiftly on the edge of the box and powered a superb volley towards goal, only to see his attempt crash off the crossbar.
Rodriguez had a golden opportunity to snatch a goal back for his side in the last 10 minutes, but sent his header wide of the mark despite having a large portion of the goal in which to aim.
Atletico continued to push further forward for an equalizer, but this proved to be the club's undoing. Goalkeeper, Asenjo, in his attempts to join find a goal from a corner kick, was terribly caught out of position. A pacey counterattack from the Russian side saw Orbaiz run through the center and have the simplest of tasks to slot home into the empty net.
Rubin Kazan now takes a vital 2-0 lead into the second leg in Russia, but Atletico will not go down easy in the defense of its Europa League crown.