The Blues missed several presentable chances before the break but were made to pay after the restart as the Championship side scored a goal on the counter-attack and added a second deep into injury time to settle the game on a frustrating afternoon for Manuel Pellegrini’s side.
Middlesbrough arrived in fine form, mirroring City’s run of just one defeat in 15 matches. Defensively sound and well-organised, anybody in the sell-out Etihad crowd expecting a Saturday afternoon stroll for the champions were setting themselves up for a disappointment.
The Blues looked spritely and undoubtedly the better team in the opening half-hour with no obvious signs of fatigue from the much discussed long-haul flight back from Abu Dhabi less than 24 hours earlier.
Pellegrini made four changes from the side beaten by Arsenal last week but, true to his word, it was another very strong line-up for a cup competition that City clearly have designs on.
The Blues made the best opportunities in the opening third with Sergio Aguero shooting narrowly wide before Tomas Mejias saved well from James Milner and then Dedryck Boyata had two bites at the cherry from close range – the second effort needing clearance from air traffic control.
Then Mejias denied David Silva from 20 yards and before beating out a fierce shot from Stevan Jovetic as the Boro keeper almost single-handedly kept his side in the game during the first half.
The teams went into the break level, but the chances created by City suggested it was just a matter of time before the deadlock was broken – and eight minutes into the second period it was – but the goal was scored by the visitors, not the hosts.
There seemed little initial danger when a ball through the middle but when Albert Adomah managed to toe-poke the ball past Willy Caballero, Fernando raced back to clear only for the ball to be charged home by Patrick Bamford to send the travelling hordes wild.
The away end in raptures has not been an uncommon sight in recent weeks and of the last 13 goals scored at the Etihad, eight have been scored by visiting teams.
And Boro should have doubled their lead with excellent chances just before and after the hour, with a scrambled clearance in the six-yard box ending with a Grant Leadbitter drive that Vincent Kompany bravely blocked and then Adomah’s lob clawed away by Caballero .
With the Blues on the rack, Boro again went within inches of increasing the lead when Lee Tomlin’s clever pirouette left him clear in the box but his shot struck the inside of the post with Caballero well beaten.
City needed inspiration from somewhere and quickly.
The frustration grew at City chased the game, but it was Boro who looked more likely to get the next goal and the Teessiders were unlucky not to punish the champions again when Jelle Vosse saw his volley well saved by Caballero on 74 minutes.
Two minutes from time Frank Lampard almost salvaged a draw with a deflected shot the inside of the post, but that was as near as City got on a miserable afternoon at the Etihad and when Boro scored a deserved second in injury time through Kike, a well-below par Blues could have little complaint.