Kevin Nolan had the first half-chance of the game after Taylor swung in a free-kick from the right, but the Bolton skipper was unable to get a shot in after a goal-mouth melee.
However, Taylor did put the visitors ahead on 14 minutes, sliding in at the far post and converting a mishit shot from Ariza Makukula.
Wanderers had a half-hearted handball appeal turned down by referee Mike Dean after Makukula's overhead struck Christopher Samba on the arm, but Samba knew little about it.
Gary Megson's side, who had had not scored in their previous four Premier League games, went two-up on 34 minutes, Kevin Davies providing the goal.
Allardyce felt his side won a "moral victory" against Bolton.
Gretar Steinsson slid a cross in from the right, Nolan got a touch and Davies, stealing in at the near post, had his first shot well-saved by Paul Robinson before making sure with the rebound.
Brett Emerton was booked just before half-time for a rash challenge on Steinsson before Keith Andrews sliced wide, and all in all it was a miserable first 45 minutes for Allardyce against his old side.
Blackburn dominated the early stages of the second half and when they introduced veteran midfielder Tugay and striker Roque Santa Cruz after 56 minutes, they suddenly acquired a cutting edge.
On 65 minutes, Warnock raced into the Bolton area to receive a slide-rule pass from McCarthy and clipped a shot past Jaaskelainen, who was unsure whether Warnock intended to cross or shoot.
Jaaskelainen was then forced to punch off the goal-line after a whipped free-kick from Emerton, before Blackburn were awarded a controversial penalty.
Tugay it was who played a raking ball over the top and Paraguayan striker Roque Santa Cruz appeared to control it with his hand before appearing to be brought down by Jaaskelainen.
Megson felt his players ran out of steam
Replays suggested Santa Cruz had run into Jaaskelainen, who was booked by Dean, rather than the other way round. But justice was served when Jaaskelainen saved a rather tame shot from McCarthy and Andrews was unable to score from the rebound.
However, Blackburn continued to attack in waves and Bolton's defence was breached again with four minutes remaining, with McCarthy making amends for his earlier mistake.
Emerton curled in a cross from the right, Samba's header from the edge of the area was blocked, Jason Roberts got a touch and McCarthy was on hand to poke home.
Ryan Nelsen very nearly snatched all three points at the death, but his glancing header from Emerton's cross hit the base of the post.
Blackburn boss Sam Allardyce:
It was a moral victory for us and on the second-half performance and chances we deserved to win it.
We're undefeated in seven games and it's very important to go on from here. We showed character, commitment and desire in abundance.
I thought the penalty was a straight red, Santa Roque Cruz was through on goal and he was hauled down, but Mike Dean deemed it to be a booking.
Bolton boss Gary Megson:
We're bitterly disappointed, we were two-nil up at half time and cruising, I can't remember a shot from the opposition.
But the game changed when Roque Santa Cruz and Tugay came on. They had the momentum and we didn't deal with it, we ran out of steam.
Three of our last four games were against Arsenal, Liverpool and Man Utd and a lot of teams have still got to play them. One or two sides will implode, we have to make sure we're not one of them.
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