Sven Ulreich saved Chadrac Akolo's 95th-minute penalty as Bayern Munich ground out a hard-fought 1-0 win at Stuttgart.
Robert Lewandowski gave Bayern Munich a 1-0 home win over Cologne, and a nine-point lead over second-placed Schalke who beat Augsburg.
Two penalties in the final minutes of the match saw winless Cologne capitulate as they threw away a 3-0 lead to lose 4-3 to fellow relegation battlers Freiburg.
Hamburg moved out of the Bundesliga's bottom three with a 3-0 victory at home to Hoffenheim, as Hertha Berlin won at Cologne.
Arsenal suffered their first Europa League defeat of the season as Cologne kept their qualification hopes alive with a 1-0 victory on Thursday.
Arsene Wenger was unimpressed by the awarding of a decisive penalty as his Arsenal side fell to defeat at Cologne.
Live updates as Arsenal look to stay unbeaten in Europa League Group H when they travel to Cologne.
Bayern Munich strengthened their grip on the Bundesliga title race with a 3-0 win over Augsburg.
Sandro Wagner scored twice as Hoffenheim recorded a first Bundesliga victory in five games by beating bottom club Cologne 3-0.
Cologne have been ordered to pay a settlement to Arsenal over damage caused by their supporters during the Europa League tie.
Bayern Munich swept aside 10-man RB Leipzig for the second time in a week to go three points clear at the top of the Bundesliga table.
Salomon Kalou scored one penalty and missed another as Hertha Berlin claimed a 1-1 draw at Freiburg in the Bundesliga on Sunday.
Mario Balotelli gave Nice an early lead, but it was not enough to prevent Lazio from emerging 3-1 winners at the Stade de Nice on Thursday.
Cologne's seemingly cursed start to the Bundesliga continued when Stuttgart scored in the fourth minute of injury time for a 2-1 win.
Bayern Munich lost a two-goal lead for the second successive week to draw 2-2 at Hertha Berlin's Olympiastadion.
Kevin Volland scored twice as Bayer Leverkusen returned to winning ways with a comfortable 3-0 Bundesliga victory over Hamburg at BayArena.
Borussia Dortmund leapfrogged Bayern Munich back into top spot in the Bundesliga following a 3-0 win at Hamburg.
Borussia Dortmund went to the top of the Bundesliga table as they beat Cologne 5-0 at Signal Iduna Park.
Cologne have criticised "inadequate" security measures at the Emirates after crowd issues in their Europa League tie with Arsenal.
UEFA has opened disciplinary proceedings against Arsenal and Cologne following incidents at the Europa League match on Thursday.
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