Iceland's Hermann Hreidarsson struck with a diving header from eight metres on 33 minutes as he reached a Paolo Di Canio corner before Garry Flitcroft and powered the ball past keeper Brad Friedel and through the legs of David Thompson on the line.
Charlton's third straight league victory takes them up three places to seventh in the table, while Blackburn remain 15th after their latest setback at home following defeats to Manchester City, Liverpool and Fulham since late August.
"We've got quite a few injuries at the moment so I think that was a fantastic achievement from the players tonight," Charlton manager Alan Curbishley told Sky Sports as he praised his team's spirit and singled out Di Canio's efforts.
"We'd just like to push on now and hopefully we can stay in that top half of the league, but it's a tough premiership this year and we won't be taking anything for granted," he added with one eye on the visit of Arsenal to The Valley on Saturday.
Blackburn had more of the first-half possession but could not beat impressive keeper Dean Kiely, with Andy Cole -- looking for his 250th goal in all competitions -- failing on three occasions and Steven Reid seeing a long-range effort saved.
Charlton substitute Radostin Kishishev saw his right-foot shot fly wide, while Blackburn's Turkey midfielder Tugay had his effort blocked on the hour before the visitors' Scott Parker fired a shot from 12 metres that was saved by Friedel.
Kiely was called on to make a magnificent save from a looping Thompson header on 65 minutes before Blackburn's Italian substitute Dino Baggio almost snatched an equaliser five minutes from time only to see his right-foot volley flash wide.
A frustrated Souness felt his team deserved to get something out of the match.
"We felt that we did enough to get something from tonight's game but it was the same old story for us. We shot ourselves in the foot. We made another mistake tonight. We've conceded a goal from a set piece when we knew the threat was there."
"Lady luck is not with us at the moment. It's a mixture of anger, frustration and feeling sorry for myself," he added. "My players deserve more from the games than they've got so far."