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Six-time winners City were less than 10 minutes away from going out at the fourth-round stage before goals from Phil Foden, Gabriel Jesus, and Ferran Torres.
City boss Pep Guardiola made 10 changes for the trip to the League Two side but his side was still packed with internationals.
The home team — 72 places below City in the English football pyramid — produced a stirring defensive display to keep their much-vaunted opponents at bay.
Then, minutes after Jesus had hit the post in the second half, they took the lead.
City failed to deal with the outstanding Ben Tozer’s long throw and Alfie May fired in from close range to spark celebrations among the players.
Riyad Mahrez should have equalized when put through by Foden but Josh Griffiths produced a fine save to keep his side’s lead intact.
City were finally level when Foden leveled with nine minutes left, volleying in Joao Cancelo’s cross.
Three minutes later Jesus increased City’s lead, beating the offside trap to fire in from Fernandinho’s dinked ball over the center-backs.
Torres made it 3-1 with the final kick of the game, turning in Ilkay Gundogan’s low cross.
Earlier, Arsenal, who have won the competition a record 14 times, went down 1-0 at St Mary’s courtesy of a Gabriel own goal.
In the early kick-off on the English south coast, Arsenal paid the price for a sluggish start against fellow top-flight side Southampton.
Arsenal boss Mikel Arteta made seven changes from his team’s 3-0 league win against Newcastle on Monday, with Pierre-Emerick Aubameyang and midfielder Emile Smith Rowe both absent.
Southampton, FA Cup winners in 1976, earned a well-deserved lead in the 24th minute when Kyle Walker-Peters’ ball across the six-yard area was inadvertently turned in by Gabriel.
It was the first time rejuvenated Arsenal had conceded for 508 minutes.
The visitors went close to an equalizer through Eddie Nketiah’s deflected shot but were forced to leave empty-handed.
Arteta, who won the FA Cup in August in his first season as Arsenal boss, said he was ‘really sad‘ to exit the competition.
‘We had a dream to do it again like last year and the dream today is over,” he said.
‘I am as well disappointed with the way we conceded the goal in an area where we know we shouldn’t be doing that. At the same time, I cannot fault the effort of the players.’
Southampton boss Ralph Hasenhuttl, who welcomed back Danny Ings after a hamstring injury and a positive coronavirus test in a strong line-up, was delighted with the win.
‘We had in the first half more punch and more power,’ said the Austrian, whose side briefly topped the Premier League earlier this season.
West Ham crushed third-tier Doncaster 4-0 despite multiple changes from manager David Moyes while fellow Premier League sides Brighton and Sheffield United also progressed.
AFRICA DAILY NEWS, NEW YORK