But they also saw their team lose at the Etihad for the first time in 16 months on a night they will want to forget in a hurry.
Gabriel Jesus marked his return to the starting line-up with an early goal to ensure there would be no miracle comeback by Basel.
But he and his team-mates switched off for the rest of the night and allowed the Swiss side to add City to their list of notable English scalps.
City, of course, will take their place in the quarter final draw next week – but this was not how Pep Guardiola would have wanted it.Then again, the City boss gave some of his fringe players a chance to shine and some of his big guns the night off.
Club legend Yaya Toure was given the captain’s armband on a rare start for the veteran midfielder.
Meanwhile England Under 17 World Cup hero and boyhood City fan Phil Foden was handed a first start at the Etihad by Pep Guardiola.
Meanwhile Jesus has not started a game anywhere since injuring his knee ligaments at Crystal Palace on New Year’s Eve.
He has made three sub appearances in recent weeks but this was the perfect chance to put him back in the starting line-up.
And it took just seven minutes for the young Brazilian to get back among the goals.
A low cross to the back post from Bernardo Silva missed out the keeper and gave Jesus the simplest of tap ins.
It was his 11th of the season and his first since he got the operer at Leicester way back in mid-November.
Sergio Aguero has done brilliantly in the absence of his fellow striker and has been in sensational goal-socirng form.
But you can’t help but feel the return of Jesus is timely. The Samba star’s energy will be a big boost for what’s left of the season.
City should really have added to their tally. A low cross from Leroy Sane found Bernardo but his shot was blocked by Blas Riveros.Then City’s Portuguese playmaker chipped over a cross that found Ilkay Gundogan but his volley was smothered by Tomas Vaclik.
But the visitors – who knew they were only playing for pride – drew level on the night.
Norwegian international Mohamed Elyounoussi pounced on a loose ball after a run by Riveros and smashed a low shot past Claudio Bravo.
Guardiola’s face on the bench was a picture – he was clearly unhappy that the goalscorer had been given so much space.
It was the Swiss team’s first goal on English soil in more than 260 minutes – and they could have had another soon afterwards.
Elyounoussi walted around Danilo and had a sight of goal but lost his footing at the vital moment and sliced his effort wide.
Soon after the re-start Vaclik had a rush of blood as he dashed out of his area and booted the ball straight at the on-rushing Jesus.
Luckily for the keeper, the ball looped back over his head but dropped well wide of the post.
City were in complete control but lacked their usual spark as the game drfited in the second half.
Guardiola had put a couple of his big guns in Aguero and Kevin de Bruyne on the bench just in case but resisted the temptation to throw them on.
Instead it was City’s other bright young thing Brahim Diaz who came on just after the hour to try to liven things up.
Instead it was the visitors who took the lead on the night with Elyounoussi turning provider with some good work on the right.He slipped the ball inside to Michael Lang who lashed a fierce shot into the roof of Bravo’s net from a tight angle.
It was Lang who got the winner against Manchester United in November and here he was scoring another famous goal.
Raphael Wicky’s men still needed another three to win the tie but even so they were on target for a famous win.
And with Guardiola being such a perfectionist, he did not look happy as he paced around his tehncial area.
Brahim could have levelled late on when he was found by Sane’s cross but Vaclik got down well to save.