Allardyce's decision to replace ineffectual midfielder Per Frandsen with Stelios Giannakopoulos on 31 minutes ultimately paid dividends, as, helped by some truly woeful Rovers defending, the Greek inspired the Wanderers to an incredible comeback.
After the match, the Trotters' manager said: "It was an unbelievable fightback by my players. It's a mammoth victory to come back from 3-1 down and we took our goals very well."
His dejected opposite number Graeme Souness could not hide his disappointment at his side's failure to secure all three points: "That summed up our season in 90 minutes, very good at things but very, very bad at other things.
"We did not defend well from the first ten seconds to the 92nd minute and could not cope with the simplest attacking play."
Unbelievably the game began with two goals almost straight from the whistle. A hideous error from Blackburn defender Martin Taylor allowed Kevin Davies to tee up Kevin Nolan to lash home the opener after just 14 seconds.
However, the visitors' joy was short-lived as Blackburn's Slovakian full-back Vratislav Gresko cut past Nicky Hunt and fired a glorious equaliser 90 seconds later.
The home side's American keeper Brad Friedel made a smart save to deny Emerson Thome's powerful header before Rovers striker Andy Cole was booked for what seemed to be a stamp on Hunt.
Bolton were struggling to contend with the dynamic runs of Brett Emerton and one such charge led to a goal in the 24th minute. Emerton's crossfield pass found Cole in space and his perfect pass picked out the arriving Dwight Yorke to slot home.
The Bolton fans who felt Cole shouldn't even have been on the pitch were left even more furious when, ten minutes later, the ex-Manchester United striker latched on to a poor back header from Bruno N'Gotty to beat the stranded Jussi Jaaskelainen.
3-1 and Rovers were coasting.
However, the main feature of their disappointing season so far has been tremendous inconsistency and an error by Tugay allowed Bolton a way back into the game three minutes before the break.
Youri Djorkaeff burst on to a long ball, fatally missed by Tugay, to pull a goal back with a crafty lob over Friedel from eight yards.
Allardyce had brought on Giannakopoulos midway through the first half and the Greek began to make a nuisance of himself after the break, almost scoring when Lucas Neill blocked his effort on the line and then being let in by a clever dummy, only to be tackled.
Similarly, Javi Moreno, Bolton's latest foreign recruit was thrown on and the changes paid dividends with the Trotters' equaliser.
When Hunt's cross looped high, there seemed little danger to the Blackburn backline but Davies flicked on and Giannakopoulos was all alone to beat Friedel from close range.
The visitors were rampant; Davies should have scored with a header, but hit the sidenetting before they completed their comeback with the winner.
Djorkaeff's corner bounced off a Blackburn defender and there was Nolan to fire into the back of the net with the home side in disarray.