FC Basel came from behind to inflict City's first home loss in 15 months -but the Blues still progress to the Champions League quarter-finals with a 5-2 aggregate win.
Gabriel Jesus gave City an early lead, but the Swiss champions fought back with goals either side of the break to give their travelling fans a night to remember.
City, with six changes from Sunday’s 1-0 win over Chelsea, wasted no time in taking command of this second leg tie.
All week the players and manager have been underlining there would be no complacency despite the 4-0 lead achieved in the first leg, and with just eight minutes on the clock the Blues were ahead.
Leroy Sane, who seems to be saving his best form for the final weeks of the campaign, burst past two or three challenges before sliding the ball to Bernardo Silva whose threaded low cross was tapped in at the far post by Gabriel Jesus.
On 17 minutes though, the visitors were celebrating when poor marking saw the ball fall to Mohamed Elyounoussi inside the box and his crisp low shot gave Claudio Bravo no chance.
The Etihad Stadium was stunned into silence on 71 minutes as Elyounoussi's clever reverse pass was hammered home by Michael Lang to give the visitors a shock lead.
City toiled in the time that remained, but couldn't find a way back into the game which, thankfully, was wrapped up in the first leg.
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