Russian clubs call the shots
Rubin's Gokdeniz Karadeniz scored after six minutes and Pablo Orbaiz struck deep into added time to give the Russians, who played the entire second half with 10 men after Roman Sharonov was sent off, a shock 2-0 win at Atletico.
Anzhi beat Hanover 3-1 and Zenit won 2-0 at home against five-times European Cup winners Liverpool while goals from Vladimir Darida, Frantisek Rajtoral and Stanislav Tecl helped unfancied Czechs Viktoria Plzen upset Napoli 3-0 away.
Brazilian Oscar spared European champions Chelsea's blushes late on at Sparta Prague in a 1-0 victory and Gareth Bale continued his remarkable scoring form with two superb free kicks in Tottenham Hotspur's 2-1 home win over Olympique Lyon.
Hosts Inter Milan, three times European champions, beat Champions League dropouts CFR Cluj 2-0 with two goals from substitute Rodrigo Palacio.
The win was soured by injury-prone forward Diego Milito lasting six minutes and crying as he left the pitch with a knee problem but fellow Argentine Palacio took his place with aplomb.
Atletico grew increasingly frustrated in the second half against Kazan and leading scorer Radamel Falcao hit the woodwork as the clock ticked on.
Allowing goalkeeper Sergio Asenjo forward for a last-minute corner could prove fatal for next Thursday's second leg as Spaniard Orbaiz gleefully slotted into the unguarded net with the home side's shotstopper at the wrong end of the pitch.
Samuel Eto'o, four-times African player of the year who has won the Champions League three times with Barcelona and Inter, was on target and missed a penalty in big-spending Anzhi's win at home to Hanover, a result which impressed coach Guus Hiddink.
Hulk's unstoppable swerving effort from 30 metres broke the deadlock for Zenit after 69 minutes and Sergei Semak poked home three minutes later to break Liverpool's resistance after the English club's striker Luis Suarez had spurned several chances.
Results: Inter Milan: 2 bt CFR Cluj: 0; Newcastle United: 0 drew Metalist Kharkiv: 0; VfB Stuttgart: 1 drew Racing Genk: 1; Atletico Madrid: 0 lt to Rubin Kazan: 2; Basel: 2 bt Dnipro Dnipropetrovsk: 0; Borussia Moenchengladbach: 3 drew Lazio: 3; Tottenham Hotspur: 2 bt Olympique Lyon: 1; BATE Borisov: 0 drew with Fenerbahce: 0; Levante: 3 bt Olympiakos Piraeus: 0; Dynamo Kiev: 1 drew with Girondins Bordeaux: 1; Bayer Leverkusen: 0 lt to Benfica: 1; Ajax Amsterdam: 2 bt Steaua Bucharest: 0; Sparta Prague: 0 lt to Chelsea: 1; Napoli: 0 lt to Viktoria Plzen: 3; Zenit St Petersburg: 2 bt Liverpool: 0; Anzhi Makhachkala: 3 bt Hanover 96: 1.