Dortmund earned their presence in the knockout stages in a goalless draw at home to Club Brugge.
Atletico claimed a spot in the knock-out stages beating Monaco 2-0 thanks to first half efforts from Antoine Griezmann and Koke in Madrid on Wednesday.
Porto and Schalke made it through from Group D before the Portugese side beat their German visitors 3-1 as Galatasary lost 2-0 to Lokomotiv Moscow earlier in Russia.
Barcelona claimed top spot of Group B with a 2-1 victory over a resilient PSV Eindhoven as Lionel Messi scored and created a goal for Gerard Pique in the Netherlands.
On Tuesday reigning champions Real Madrid, Manchester City, Bayern Munich and Juventus qualified.
Manchester United, Roma and Ajax also went through.
In round six, played on the week beginning December 10 Tottenham Hotspur have to match Inter Milan’s result to claim second spot in Group B but face a trip to unbeaten Barcelona and Inter welcome PSV Eindhoven to the San Siro.
In Group C three clubs in Napoli, Paris Saint-Germain and Liverpool can still make it through.
Last year’s runners-up need to beat the Italians 1-0 or by two clear goals at Anfield and all PSG have to do is claim a point away at Red Star Belgrade.
Shakhtar Donetsk and Lyon go head-to-head in Kharkiv but the Ukrainians have to overcome the visitors for the final spot from Group F.
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