The American drilled home a stunning 88th-minute finish while the visitors were still celebrating their equaliser by substitute Diouf at the other end moments earlier at The Reebok.
Owen Coyle's men had played with 10 men since Mark Davies' 56th-minute dismissal for an apparent elbow, but they still grabbed a 65th-minute lead through Fabrice Muamba.
And just when Rovers appeared to have made their desperate pressure tell, American Holden raced on to a neat header down from Kevin Davies to smash his rising shot past Paul Robinson.
It was a dramatic way for Coyle's men to bounce back after last week's disappointing loss at Manchester City, with Holden the only change in favour of Muamba, who started on the bench.
Rovers, on a high after their win over Wolves, fashioned the first chance in the opening minute with Jason Roberts flicking a cross by El-Hadji Diouf just wide.
But Coyle's men soon grew into the occasion and began to look the better side, with Mark Davies drilling a low shot at Robinson and Morten Gamst Pedersen's cross almost finding Martin Petrov.
Petrov turned provider to fire in a superb low cross in the 10th minute, with the stretching Kevin Davies almost connecting on the edge of the six-yard box.
A mazy run from the impressive Petrov ended in a low shot the wrong side of Robinson's right-hand post in the 21st minute as Bolton continued to press.
An incisive through-ball by Bolton defender Paul Robinson sent Johan Elmander tearing clear down the right flank only for him to be tripped by Phil Jones, who was booked by referee Mark Clattenburg.
But Blackburn improved as the half went on. Roberts almost raced clear on to a Jones through-ball after 34 minutes but was pulled down by Zat Knight, who was fortunate to escape with a booking.
Then Pedersen's dangerous free-kick looped over the Bolton wall and was parried by Jussi Jaaskelainen into the path of Gael Givet, who headed horribly wide from the corner of the six-yard box.
Tempers began to fray in a ragged start to the second half after Gary Cahill had seen a shot blocked at point-blank range and former England goalkeeper Robinson parried well from Holden.
Davies was issued a second yellow card by Clattenburg for his apparent elbow on Jones, then Martin Olsson and Johan Elmander were booked in quick succession.
Rovers sought to exploit their extra man advantage with Christopher Samba's header booted off the line by Kevin Davies, and Givet firing the rebound high and wide.
Bolton grabbed the lead out of nowhere when substitute Muamba - with virtually his first touch of the match - finished superbly when afforded too much space on the right.
Rovers' push for an equaliser left space at the back and Kevin Davies almost capitalised when he directed a Petrov cross just wide in the 75th minute.
Rovers did grab their equaliser three minutes from time when a superb back-header by Roberts played in Mame Biram Diouf to squirt a left-footed effort past Jaaskelainen.
But the home side grabbed the points straight after the restart when striker Davies headed a long ball into the path of Holden, who controlled superbly before lashing his winner past Robinson.