First-half substitute leaves it late to book a place in the last four as visitors continue to be in the running for all competitions
The Gunners will feel hard done by after shading most of the encounter, but the 83rd minute breakaway goal means it is Roberto Mancini's side who move into the last four with their first win away to Tuesday's opponents for 36 years.
In a frenetic start to the game, both sides had chances to open the scoring within the first 10 minutes.
First it was the visitors who went close when winger Adam Johnson cut in from the right-hand side before unleashing a dipping left-footed strike. A few inches lower and goalkeeper Lukasz Fabianski would have been left stranded.
In response, the hosts went even closer to opening the scoring. Park Chu-Young’s shot from close-range produced a glorious save from Costel Pantilimon and Stefan Savic made sure it wasn’t going to trickle in by hacking the ball away to safety.
Pablo Zabaleta shot wide from distance as City looked to take control early in the game but his attempt sailed wide of the post. England Under-21 star Alex Oxlade-Chamberlain caused mischief throughout the match and had most of the players he took on backpedalling.
The first was Nigel de Jong, who didn’t know which way the teenager was going to go. He stood off him allowing the youngster to have a pop from 25 yards which again produced a stunning save from Pantilimon.
Samir Nasri generally struggled on his return to the Emirates as the Gunners faithful made sure he had an unwelcome reception as they booed him every time he touched the ball.
City made a substitution in the first half, bringing on striker Aguero for Aleksandar Kolarov, who didn’t seem happy that he was being replaced just half an hour into his night.
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The second half opened with the same pace as the first, striker Edin Dzeko making goalkeeper Fabianski scramble across his line with a curled effort that didn’t have enough finesse on the shot.
Oxlade-Chamberlain produced another fine drive from range. This time it was the turn of Zabaleta to stand off him when the youngster cut in from the right before stinging Pantilimon’s hands as the shot stopper punched clear.
Former England midfielder Owen Hargreaves tried to score from outside the box but he shot high into the crowd behind the goal before Chamakh had an attempt at the other end which went as wide as Hargreaves’ had gone high.
Oxlade-Chamberlain tried for a third time to beat Pantilimon but shot straight at the goalkeeper in the most tame of his trio of attempts.
Then, Aguero finally opened the scoring with seven minutes remaining, with the move taken directly out of the Arsenal textbook. The hosts were dispossessed from their own corner and the ball was taken out wide by Edin Dzeko.
He ran down the touchline and into the middle of the park in a swift break before cutting the defence open with a through ball to Adam Johnson. The winger's clever flick set up Aguero, who slotted past Fabianski with a neat finish into the bottom corner.
Arsenal rallied as they looked for an equaliser to send the tie into extra-time, but Gervinho's whipped cross just evaded the head of Chamakh in stoppage-time as the visitors claimed a place in the last four.
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