Mark Hughes shuffled his pack, replacing Roque Santa Cruz, Vincent Kompany and Nigel de Jong with Emmanuel Adebayor, Kolo Toure and Stephen Ireland, but they were unlucky to go behind after 18 minutes after Joleon Lescott was adjudged to have handled Tyrone Mears' cross.
The controversial decision sparked the game into life and Graham Alexander's penalty, which went underneath Shay Given's outstretched arm and into the left corner of the net, stoked the fires of injustice in the City crowd who gave referee Stuart Attwell a torrid time for the remainder of the game.
The visitors were fulling deserving of their second goal, however, and Steven Fletcher was given the easiest of tap-ins after Chris Eagles capitalised on an incisive Burnley counter-attack on 32 minutes to leave Lescott in his wake and deliver a cross between the luckless defender and Given.
Shaun Wright-Phillips delivered a spark of hope at half-time when he bamboozled Robbie Blake and hacked a hopeful shot towards Brian Jensen, but his effort deflected off Stephen Jordan's outstretched back leg and wrong-footed the Burnley keeper before creeping in at the back post.
The City goal was the least they deserved for all their hard work but two quick second-half goals gave City an unexpected lead.
Toure came up for a 55th minute free-kick taken by Gareth Barry and found himself scoring the equaliser after Lescott arrived with a cross from the far post.
Before the home crowd had fully digested that goal, City found themselves in front after Wright-Phillips' right-wing cross was converted on the half-volley by Craig Bellamy two minutes later.
With their visitors reeling, City had over half an hour to make sure of a win but Adebayor and Carlos Tevez spurned a succession of chances to put the game beyond the visitors including a wild pointblank lash from Tevez just before he was substituted.
Substitute Kevin McDonald finally made City pay for their profligacy with three minutes to go when he latched onto Fletcher's headed knockdown and scored a memorable - and probably deserved - equaliser for Burnley in front of his own fans.