The Gunners needed only a point against Napoli on Wednesday night to be sure of top spot in Group F and with it seeding for the knockout stage.
However, after their 2-0 defeat at the Stadio San Paolo coupled with a late winner for Dortmund in Marseille, Arsene Wenger's men are now likely to face one of Europe's leading sides such as Barcelona, Bayern Munich, Real Madrid or Paris St Germain in Monday's draw.
Flamini, though, feels Arsenal should be proud they made it through to the last 16, with Rafa Benitez's side now having to continue their campaign in the Europa League.
"It was one of the hardest (groups) because you have a team like Napoli who have not qualified and we have finished second, level with them on 12 points," Flamini said, quoted on www.uefa.com.
"We will play a big team (now), but we knew that. Anyway, if you want to go to the final and try to win something, you have to play all the big teams.
"I do not really have a preference, so we will see what happens with the draw."
Gonzalo Higuain, who was a summer transfer target for Arsenal, slotted home on 73 minutes to finally break the visitor's determined resistance.
After midfielder Mikel Arteta was sent off for collecting a somewhat soft second yellow card, it was always going to be an uphill battle for the Barclays Premier League leaders to get back into the tie, which was settled when Jose Callejon chipped in a second during stoppage time.
Arsenal now face a test of their domestic credentials when they travel to Manchester City on Saturday lunchtime, before hosting Chelsea on December 23.