Substitute Paul Konchesky fired The Addicks into the lead just before the hour but David Thompson levelled matters just 38 second later with an equally sound strike.
Richard Rufus restored Charlton's advantage and Jason Euell eased the growing nerves as his late effort made the game safe in injury time.
The win gives The Addicks some welcome space away from the bottom three as the majority of the basement sides had negative results at the weekend.
A scrappy opening to the game saw few clear cut chances, with only Jason Euell for the hosts looking menacing with his run down the left.
Nils Eric Johansson then had to clear from his own line after Alan Kelly's punch had gone straight to Radostin Kishishev.
Andy Cole then looked to have a legitimate shout for a penalty when Jonathan Fortune slid in on the former Manchester United man without touching the ball, although referee Uriah Rennie waved away Cole's appeals and gave a goal kick.
Cole turned well again on the half hour after he miss-controlled the ball and managed to get his shot in on the turn but it went just wide of Dean Kiely's post.
David Thompson was then twisting and turning inside the box five minutes later but poked his hurried effort high and wide of the target.
Cherlton went close on the stroke of half time as Shaun Bartlett arrived at the near post from a corner but the South African glanced his header just wide of the target.
A minute after the restart Norwegian international Egil Ostenstad drove in behind the defence and hit is first effort at Kiely before heading the rebound against the foot of the post.
Paul Konchesky, who came on as substitute at half time, then made his mark in the 59th minute by breaking the deadlock with a superb free kick.
Andy Todd brought down Scott Parker 25 yards out and Konchesky fired the ball in left footed into the top corner giving Kelly no chance.
Amazingly, Blackburn hit back instantly and David Thompson had levelled the scores with a cracking strike half a minute later.
The former Liverpool man flicked the ball on to Cole who laid the ball off for Thompson to fire in a stinging low drive that flew past Kiely and nestled in the bottom corner.
Kevin Lisbie missed a glorious chance to restore Charlton's lead when he lifted Euell's excellent cross over the bar from close range.
The home side went back in front in the 73rd minute when Richard Rufus lost his marker to nod in from a corner.
The big centre half eluded his man to float his header into the corner of the net, where a man on the post would have surely cleared the danger.
Euell made the game safe in the dying moments when he raced onto a Bartlett flick on and flashed in a wicked drive from 20 yards that flew past Kelly into the back of the net.
Match summary:
Charlton v Blackburn
