Aguero netted his second goal of a dramatic encounter with just three minutes left at rain-lashed Loftus Road, but this was another alarmingly sloppy display from the struggling Premier League champions.
Manuel Pellegrini’s team were well below their best again just three days after suffering a shock home defeat against CSKA Moscow that left them in danger of elimination from the Champions League.
Charlie Austin had given QPR a deserved early lead and it needed an Aguero equaliser tinged with controversy to level the score before half-time.
A Martin Demichelis own goal in the closing stages put second bottom QPR back in front, but Aguero remains the one bright spot in a difficult campaign for City and he came to their rescue in the final moments.
Aguero’s heroics couldn’t hide the latest in a growing list of underwhelming City displays and they need to improve quickly to catch leaders Chelsea, who are now eight points clear of their title rivals.
Pellegrini made four changes following the midweek defeat to CSKA, with Bacary Sagna, Fernandinho, Eliaquim Mangala and Samir Nasri in for Pablo Zabaleta, Stevan Jovetic, Vincent Kompany and James Milner.
But the champions looked bedraggled and befuddled as QPR ran riot in the early stages.
Austin had the ball in the net in the eighth minute when he headed home from close-range, but the QPR forward had strayed several yards offside.
Remarkably Austin was denied again in bizarre circumstances from the restart.
Joe Hart hit his free-kick straight to Austin, who fired home and wheeled away in celebration only for referee Mike Dean to disallowed it because the City goalkeeper had broken the rules by accidently kicking the ball twice.
Yet City failed to heed the warning of their fortunate escapes and Austin finally made them pay for some more shoddy defending in the 21st minute.
Eduardo Vargas tricked his way past Gael Clichy and cut in from the right before sending over a low cross that Austin, played onside by the ponderous Mangala, met with an emphatic strike past Hart.
– City lethargy –
Yaya Toure, criticised for some lacklustre displays so far this season, lifted City out of their lethargy with a curling shot that flashed just over.
Suddenly there was more menace about City and they drew level in ruthless fashion in the 32nd minute.
Once again QPR had a grievance with the officials as Aguero made a run from a marginally offside position to brilliantly control Mangala’s long pass with a deft touch as it looped over his head.
Aguero then used the slightest touch off his arm to knock the ball down for a cool finish past Robert Green.
Toure was inches away from turning in Nasri’s cross in the opening moments of the second half.
Pellegrini sent on Edin Dzeko as he looked to snatch a winner, but the Bosnia striker lasted only four minutes before limping off to be replaced by Frank Lampard.
That setback foreshadowed more pain for City as Harry Redknapp’s team were gifted their second goal in the 76th minute.
Austin whipped over a cross and when Demichelis challenged with Zamora, the Argentine defender headed into his own net.
City responded with a sustained assault on Green’s goal and Richard Dunne cleared off the line to foil Aguero after Joey Barton’s woeful backpass.
But Aguero wouldn’t be denied and he levelled in the 83rd minute with a typically clinical finish.
Toure clipped a pass through to Aguero and he showed great composure to jink around Green before cutting back to make space for a powerful shot into the corner.