The Argentina international netted twice for salvage a draw for Manuel Pellegrini's side, who are now eight points behind Jose Mourinho's men
The Argentina international cancelled out Charlie Austin's opener before equalising again with seven minutes remaining after Martin Demichelis’ own goal had given Harry Redknapp's side their second lead of the match.
Austin also had two disallowed goals before the break, while City, who were lacklustre in large parts at Loftus Road, are now eight points behind Premier League leaders Chelsea.
Following Wednesday’s 2-1 defeat to CSKA Moscow in the Champions League, Manuel Pellegrini made four changes to his side as Eliaquim Mangala replaced injured captain Vincent Kompany at the heart of the City defence.
A reshaped City backline, which also featured Bacary Sagna in place of Pablo Zabaleta, soon looked vulnerable and Austin found the net twice in quick succession, only to have both efforts disallowed.
The striker headed home from a clearly offside position and, from the resulting free-kick, City goalkeeper Joe Hart hit the ball with his standing foot before mis-kicking to Austin.
Hart's failure to kick the ball directly out of his area meant a re-take was necessary, despite a fine finish from the former Burnley forward, but City were visibly unsettled and Hart was forced to deny Austin from close-range in the 15th minute before the strikefinally got his goal.
Gael Clichy charged towards Mauricio Isla and lost his footing, which allowed the Chile international to find Austin, who was played marginally onside by Mangala and slotted home.
A dreadful spell from City followed, littered with careless passing. Aguero appeared the only visiting player free of the malaise and there was quality and fortune on display when he hauled his misfiring side level.
Playing, like Austin, on the shoulder of the last man, Aguero wonderfully brought down Mangala's raking pass but the ball struck his hand as he controlled before beating Robert Green.
Nevertheless, QPR finished the half on top as Hart denied Austin once more following an error from Fernando.
Isla made a vital intervention to stop Aguero converting Jesus Navas' low cross from the right channel in the first minute of the second period, before Yaya Toure came agonisingly close to converting a move he launched down the opposite flank.
City belatedly found slightly more control in possession but a last-ditch interception was required from Fernando in the 62nd minute, with Zamora poised to restore QPR's lead.
Edin Dzeko departed with an injury only four minutes after coming on as a substitute and City's misery appeared complete when Demichelis put Austin's cross into his own net under pressure from Zamora in the 76th minute, after Fernando had gifted possession to Eduardo Vargas.
Again Aguero led a lone charge for the visitors, rounding Green only to see Dunne clear his shot from the goalmouth. Dunne's centre-back partner Steven Caulker then nodded a header from replacement James Milner off the line, and Green was forced to deny Toure in the 80th minute.
But Aguero secured a point for City with his second of the game after he latched on to Toure's long ball, rounded Green, and steered his effort past Isla on the line.