Mark Davies gave the visitors the perfect start with his fifth-minute opener and Nigel Reo-Coker doubled Bolton's lead on the half hour.
Aiyegbeni Yakubu did pull one back for Rovers in the middle of a much improved second-half display, but it was not enough.
Bolton leapfrogged Blackburn at the bottom of the Premier League table as a result.
Already under intense scrutiny, with the local paper calling for his head on Monday, Kean was roundly abused by the home fans from the moment Davies struck.
Only one side has avoided being relegated in May having been bottom at Christmas, and it is hard to see the Scot inspiring Blackburn the way Bryan Robson famously did at West Brom.
As the first-half drew to a close, it was hard not to feel sorry for Kean.
All alone in the technical area, in the rain, he cut the figure of a very lonely man.
The Rovers fans had abandoned their two-game pledge to get behind their players on Saturday, just as Peter Odemwingie's shot hit the back of the net to condemn them to another defeat against West Brom.
And any hope of the fragile peace being restored was wrecked after just four minutes.
It had already become clear Bolton were more atuned to the task in front of them when Christopher Samba made a hash of a clearance and David Ngog had enough space inside his box to regain his feet and slide a pass back to Davies.
The midfielder had not scored for over a year. On this occasion, his aim was true and he found the bottom corner, beyond the despairing grasp of Paul Robinson.
Cue the anti-Kean venom, which came rippling down the stands from all sides.
The response was a good deal more passionate than anything Kean's players could muster.
Shorn of a full defence due to injury, Rovers were a pitiful sight.
Gary Cahill, named skipper after Owen Coyle took the brave decision to axe Kevin Davies, screwed a glorious chance to double Bolton's lead wide.
But it was only a matter of time before the visitors struck again.
Ivan Klasnic's deft touch found Reo-Coker, who continued his forward charge after releasing Martin Petrov down the left.
When Reo-Coker collected the cross, he had his back to goal. But he got the better of Morten Gamst Pedersen far too easily and, yet again, Robinson was beaten to his bottom corner.
The response was predictable.
Watching from the comfort of his home, Manchester United striker Michael Owen found it particularly distasteful, as he outlined on Twitter, although the Rovers fans did, at times, widen their abuse towards their owners, Venky's, who they blame for all the mess.
The Bolton contingent gleefully made it worse, chanting 'You should have kept Big Sam' in honour of their former boss, sacked by Blackburn 12 months ago to make way for Kean. Their Blackburn counterparts quickly joined in.
It was unpleasant to say the least, and the noise continued as soon as Kean returned for the second-half.
His team came so close to giving him something to shout about though, with Junior Hoilett pulling the ball back to Steven Nzonzi, whose effort flew just over with Jussi Jaaskelainen nowhere.
It was the start of a far better period for Rovers, who pulled one back midway through the half when Hoilett cut in off the left flank and found Yakubu with a slide-rule pass that invited the neat finish.
Rovers piled forward looking for the equaliser, with Samba going close and a couple of Hoilett crosses fizzing across the box.
But the second would not come. And in truth it probably would not have mattered anyway as the Rovers fans unleashed more anger at the final whistle.
Kean waited for a while, then turned, took a quick look skywards, and walked away. With trips to Liverpool and Manchester United ahead, maybe for the last time.