The Spanish outfit did control proceedings in the first period, but stern defending from Rubin restricted them to few clear-cut chances.
Both sides had chances in the second period, with Radamel Falcao scoring late on, but it was not enough to book Atletico's spot in the next stage.
Read how it all unfolded in Sports Mole's minute-by-minute live commentary of the action below.
RUBIN: Ryzhikov; Kuzmin, Navas, Marcano, Ansaldi; Orbaiz, Kislyak, Eremenko, Karadeniz; Natcho, Rondon
ATLETICO: Asenjo; Manquillo, Miranda, C.Diaz, Cisma; Suarez, Saul Niguez; Rodriguez, Garcia, Adrian; Falcao