Bayern Munich were held to a 1-1 draw by Schalke, while Bayer Leverkusen ran out 4-2 winners against Hertha Berlin.
Bayer Leverkusen twice came from behind to beat Hertha Berlin 4-2 at the BayArena and maintain their perfect start.
Emergency keeper Cosmin Moti saved two penalties as Bulgarians Ludogorets Razgrad made the Champions League group stage.
Liverpool face holders Real Madrid in the Champions League while Manchester City are again grouped with Bayern Munich.
Andre Villas-Boas is targeting a "spectacular" return to the Champions League with Zenit St Petersburg.
Bayer Leverkusen claimed a shock 2-0 Bundesliga win at Borussia Dortmund on Saturday, while Hannover beat Schalke.
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