Tottenham, Manchester City and Chelsea are all through to the second round of the competition.
The move to their new Wanda Metropolitano stadium was created to herald a fresh period of success for Atletico Madrid, but Diego Simeone's side's streak of four straight runs to at least the Champions League last eight was abruptly ended.
Robert Lewandowski opened the scoring and Corentin Tolisso struck twice as Bayern Munich fell just short of topping Group B with a 3-1 win over Paris Saint-Germain at the Allianz Arena.
Stephan El Shaarawy warned Roma to ignore Chelsea-Atletico Madrid and focus only on Qarabag.
The Italian champions go through behind Barcelona, who rounded off their group phase by easing to a 2-0 win at home against Sporting Lisbon.
Who's into the knockout stage?
The English have never had five teams in the knockout stage of the Champions League.
Dortmund, which reached the final in 2013, is already out after failing to win any of its group games and is now competing with APOEL for the consolation of Europa League qualification from Group H. Ahead of its visit to Real Madrid on Wednesday, Dortmund has just two points from five games, the same as Cypriot team APOEL. If Porto finish level on points with Leipzig, the Portuguese side will qualify due to their better head-to-head record.
Sevilla only need to draw with Maribor in Slovenia to qualify for the knockout stage, and would go through as group winners if they win and Liverpool slip up.
In that case, United would still win the group, unless they lost by five goals but would still qualify, unless they lost by seven goals.
Benfica are yet to pick up a single point and will therefore finish bottom of the group no matter what happens on Tuesday. The Parisians won the first game against Bayern 3-0, and the Bundesliga team will have to win by a four-goal margin to finish top.
Roma knew they would go through from Group C with a win, which they got, although they could only edge out Qarabag of Azerbaijan 1-0 at the Stadio Olimpico with a Diego Perotti effort in the second half.
"We want to win and sing together", Di Francesco posted on social media.
The Premier League side equalised in the 64th minute when Lukaku ended his goal drought, showing great strength to hold off his marker before firing a left-footed shot home.