Twenty seconds remained of the three minutes added to the end of the match when Henrik Pedersen attempted to lift the ball over Richard Dunne, succeeding only in striking it against the defender's outstretched arm. So clear-cut was the decision that City players did not even protest as Gary Speed strode up and drilled the ball past David James.
The timing of the decisive penalty was hard enough to swallow but, to all save the few thousand travelling Wanderers fans, the result was pure larceny. City struck the woodwork five times and the Bolton goalkeeper Jussi Jaaskelainen turned in an early contender for performance of the season as Bolton inflicted the first defeat upon Stuart Pearce since his debut as City's manager in March.
"We found it difficult after playing in Europe on Thursday," said Allardyce. "The good old woodwork did us a huge favour and we had some excellent goalkeeping. We've got something we didn't deserve, but deserved or not, we've got it. Sometimes, when you're on the receiving end of something like this, you can see it coming and I think Stuart saw it coming."
The defeat also halted a start to the season that saw Pearce named manager of the month before the game and had City fans entertaining giddy thoughts but a statistic that will bring them down to earth is that since moving to their new City of Manchester Stadium home, their team has won just 14 of 41 Premiership games and the atmosphere is so quiet that the club has resorted to piping in crowd noise over the public address system, even during play.
Not even the introduction of "Freddie" Flintoff pre-match could lift the crowd during the early stages of a contest that threatened to be dour as Allardyce set out his stall to grind out a point, with the dim hope of a breakaway goal.
Yet, to the credit of the home supporters and their players, so dominant was City's performance that, by game's end, there was no need for artificial backing as they willed on their team.
Kevin Davies wasted Bolton's first and, until the penalty, only chance when he placed a free header at James in the 18th minute but, thereafter, the traffic flowed exclusively one way and, in the 32nd minute, Antoine Sibierski's header struck the crossbar, ricocheting high and returning to earth via the same piece of woodwork.
It was the start of a sequence of almost farcical missed opportunities for City, with Jaaskelainen ending the half with a brilliant save, tipping over another Sibierski header.
Soon after the interval, Joey Barton curled a shot against the post, the keeper stuck out a boot to make a stunning save from Claudio Reyna, similarly denied Darius Vassell, then saw Kiki Musampa and Sun Jihai both hit the crossbar before the dramatic finale.
Goals: Speed pen (90) 0-1.
Manchester City (4-4-1-1): James; Mills, Dunne, Distin, Thatcher; Sinclair (Jihai, 25), Barton (Ireland, 81), Reyna, Musampa; Sibierski; Vassell. Substitutes not used: De Vlieger (gk), Fowler, Onuoha.
Bolton Wanderers (4-3-3): Jaaskelainen; Ben Haim, N'Gotty, Jaidi, Pedersen; Speed, Diagne-Faye (Campo, 45), Nolan; Diouf (Nakata, 56), Davies, Giannakopoulos (Gardner, 65). Substitutes not used: Walker (gk), Borgetti.
Referee: M Dean (Cheshire).
Booked: Bolton Wanderers Davies.
Man of the match: Jaaskelainen.