The other two English sides had, on the face of it, easier draws for the first knockout round with Jose Mourinho's Chelsea facing their former striker Didier Drogba's Galatasaray, while David Moyes' Manchester United take on Greek champions Olympiacos.
City may have paid a steep price for failing to top their group but in the build-up to the draw at UEFA headquarters in Nyon, Switzerland, were the one team that Barcelona had been keen to avoid - the local sports daily El Mundo Deportivo's front page had stated simply "El City, No!"
City boss Manuel Pellegrini famously made a mathematical error in the final group match, not realising that one more goal at Bayern would have seen his side top the group and be seeded for the draw, but the club's director of football Txiki Begiristain - formerly of Barcelona - said the team is brimming with confidence.
Begiristain told the club's website: "I think it will be a great match. Ours is a team with a lot of confidence especially after winning against the champions in Munich - that will give us a lot of confidence. Not just at home but away as well.
"We are showing that we can score in all matches. This is important in the Champions League. We scored in Plzen, in Moscow, in Munich - it should give us confidence to play against a team who have been champions many times.
"Our manager knows perfectly Barcelona because he managed in Spain for a long time. In this sense, we are confident."
Begiristain said the text messages "will be flying" between Argentina team-mates Lionel Messi and Sergio Aguero, and added: "If you want to win the Champions League you have to beat the biggest teams, Barcelona are one of the biggest teams."
Arsenal beat Bayern 2-0 in Munich at the same stage last season but went out on away goals - the German side having won 3-1 at the Emirates.
Gunners winger Alex Oxlade-Chamberlain said: "We managed to get a good result away at Bayern last season so that brings back good memories. If you're going to do well in the competition you've got to beat the best teams."
Arsenal now have German international playmaker Mesut Ozil in their ranks and Bayern defender Jerome Boateng admitted: "They're the toughest opponents we could have had. They'll be totally up for it after what happened last year. Both matches will be very intense."
Drogba said he was relishing his match against Chelsea, having scored the equaliser and then the winning penalty against Bayern Munich to win the competition in 2012.
"What a draw... I'm the luckiest man in this competition," he said on his official Instagram account. "In both games I'll be playing home! See you in few months."
Chelsea midfielder Juan Mata said it would be a fond reunion for all concerned.
He told the official Chelsea website: "Didier was a legend here. I guess that he would be very excited about coming back. He did a lot of great things for this club and scored a lot of very important goals. In fact, he scored probably the most important goals in the history of this club."
In other matches, Real Madrid face German opposition in the form of Schalke 04, last year's runners up Borussia Dortmund take on Zenit St Petersburg, AC Milan will play in-form Spanish side Atletico Madrid while Bayer Leverkusen face big-spending Paris Saint-Germain.
John Alexander, Manchester United's club secretary, said the Premier League champions' straightforward draw highlighted how important it had been to win their group.
He told uefa.com: "If you look at the ties Arsenal and City got, that shows why you have got to win the group. Whoever came out of the pot would have been a good one to draw. United are a big club in Greece so we will have a good following over there."