Manuel Pellegrini made four changes for the visit of the Championship side, with Sergio Aguero continuing his return to fitness, but the hosts were lacklustre for the majority with a mix-up in defence handing the game to the visitors.
Fernando over-cooked a backpass to Willy Caballero, which the goalkeeper just manages to clear only for the midfielder to hit his own clearance straight into Patrick Bamford.
As City pushed for a late equaliser, Middlesbrough, who were successful on the counter all game, put the game to bed as Kike slotted home in stoppage time.
