Copenhagen held Bayern Munich to a 0-0 draw away on Wednesday, the visitors needing a VAR review to overturn a penalty awarded to the home side in injury time.
Bayern, who scored two late goals to come from behind and win 2-1 in Denmark in October, looked to turn the game late again when the referee pointed to the spot in added time for a handball against Frans Kraetzig.
After a VAR review showed contact with the upper arm and shoulder, referee Stephanie Frappart withdrew the penalty, despite the protests of striker Harry Kane and home manager Thomas Tuchel.
Despite Bayern dropping points in the Champions League group stages at home for the first time since 2018, the German champions qualify for the last 16 in first place.
The result, combined with Manchester United's 3-3 draw at Galatasaray, means Copenhagen sit second in the group with a match remaining.
The Danish side can qualify for the last 16 for just the second time in their history by avoiding defeat at home to Galatasaray in December.
After making no substitutions in the weekend's win over Cologne despite complaints about player strain, Tuchel shuffled his deck, benching Leroy Sane and Serge Gnabry, but keeping Kane up front with first place secured.
A hip complaint ruled Kim Min-Jae out, pushing midfield stalwart Leon Goretzka into central defence, while veteran Thomas Mueller was given a first Champions League start of the campaign.
Kane was quiet early on, but Bayern had several early chances, Mueller and Mathys Tel, the France teenager 16 years his junior, building a budding partnership up front.
Mueller created an early chance for Tel only for the teenager to blast over, scuffing his shot with his shin.
Tel then found Mueller directly in front of goal, but the 2014 World Cup winner's attempt was kept out by a desperation save from Kamil Grabara.
Grabara was on the spot again midway through the second stanza, keeping a Kane shot out of goal with his fist.
Mueller, playing 90 minutes for just the second time this season in all competitions, went down in the box late under attention of the visiting defence but the referee waived his claims of a penalty away.
Through to the knockouts for the 16th straight year, Bayern will travel to Manchester in December, with the hosts sitting last in the group.
Despite the draw, Bayern continued their unbeaten run in the group stage to a record 39 games.
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