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The two sides could only be separated by goal difference going into the game, but Schalke’s second 1-0 win of the season over Bayern, thanks to a Lincoln free-kick after 69 minutes, saw them move clear at the summit.
Borussia Dortmund failed to alleviate their fans’ concerns about off-field problems as they slipped to a 2-0 home defeat to 10-man Stuttgart.
Top scorer Jan Koller returned to Dortmund’s starting line-up following a lung infection, but he was the fall guy as he failed to cancel out Silvio Meissner’s 43rd minute opener by missing a 48th-minute spot-kick, for which Fernando Meira was dismissed.
Dortmund may have had Christian Worns sent off too, allowing Silvio Meissner to clinch the points from the penalty spot, but that was in the final minute.
Champions League chasing Werder Bremen and Bayer Leverkusen were both held to draws on Saturday, while Hansa Rostock beat Bochum 3-1 for their first home triumph of the season.
Werder Bremen, destroyed 7-2 by Lyon during the week to seal a humiliating 10-2 aggregate defeat in the Champions League, could have done their chances of qualifying for next year’s competition a world of good, but managed only a goalless draw at home to Mainz.
Leverkusen, also eliminated from Europe’s elite club competition in midweek by Liverpool, played against the 10 men of Hertha Berlin following the 12th minute sending-off of Dick Van Burik, but needed a late Andrej Voronin strike just to grab a point and a 3-3 draw.
They are four points behind third placed Bremen.
Robson Ponte put Leverkusen into a fifth-minute lead and their penalty-taking goalkeeper Jorg Butt, following Van Burik’s red-card for taking Voronin’s back leg away from him, drove home the spot-kick for a 2-0 advantage.
Marcelo Marcelinho scored twice in six first-half minutes to pull Hertha level, though, and Andreas Neuendorf gave the Berliners a 3-2 lead early in the second half. But Voronin struck six minutes from the end to give Leverkusen a draw.
Hamburg are up to fourth in the standings - just one point behind Bremen - after a 4-3 triumph at Arminia Bielefeld.
Hamburg took an early lead through Benjamin Lauth, but Massimiliano Porcello and Fatmir Vata scored to put Arminia in front.
The visitors showed their European credentials by fighting back in style, though. First-half strikes from Sergej Barbarez and Khalid Boulahrouz, coupled with a fourth goal by substitute Mehdi Mahdavikia, made the prolific Delron Buckley’s last-gasp effort nothing put a consolation.
Miso Brecko’s late sending-off ensured Hamburg finished the match with 10 men.
Two goals in four minutes shortly after the half-time interval steered Hansa Rostock to their first home win of the season at the expense of fellow strugglers Bochum.
Antonio Di Salvo’s second of the match in the 49th minute was followed by Rade Prica’s 53rd minute goal. Edu’s strike was mere consolation for Bochum, who lost 3-1.
Rostock leapfrogged Bochum to leave them second-bottom. The winners are still seven points adrift of Mainz, who occupy the last position of safety.
Kaiserslautern got a goal on the stroke of half-time from Halil Altintop to beat Borussia Monchengladbach 1-0.
Juan Carlos Menseguez struck in the sixth minute as Wolfsburg edged Hannover 1-0.
Two late goals from Bundesliga top scorer Marek Mintal fired Nurnberg to a 3-2 win at bottom club Freiburg, leaving the cellar dwellers 11 points from safety.
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