The Frenchman, frustrated by his lack of starting opportunities this season, drove home from a free-kick with 15-minutes left on the clock after squandering countless chances.
Rovers were reduced to ten-men in the first half when defender Zurab Khizanishvili was giving his marching orders for a foul on Cisse.
For the Reds, seeking to recover from the Chelsea mauling a fortnight ago, Sami Hyypia was an unexplained absentee from the 16-man squad. Djimi Traore joined skipper-for-the-day Jamie Carragher at centre-half. The impatient Cisse was handed a start alongside Peter Crouch.
Following the inconvenience of an international break in which Liverpool lost influential captain Steven Gerrard and saw Anfield favourite Peter Crouch receive a disgraceful reception at the hands of England fans, the club must have been delighted to return to Premiership action, seeking to rebuild confidence following a difficult start to the campaign.
But after three straight wins, Rovers' boss Mark Hughes would also have been delighted to get back to domestic business. The Welshman welcomed countryman Robbie Savage back from suspension, but Craig Bellamy failed to recover from injury meaning a start for Shefki Kuqi, who scored both goals in the 2-0 win over West Brom.
After a disjointed opening, it was Cisse who had the first chance to break the deadlock, but wastefully tried an acrobatic volley rather than opt for a free header from six-yards out. Carragher headed just wide moments later.
But Liverpool seemed unduly rushed. Passes went astray, rash tackles went in and Gerrard's absence was sorely apparent. But Rovers were little better, in a strangely subdued Anfield atmosphere. The anxiety levels at Anfield are reaching fever pitch.
Capitalising on some woeful Liverpool passing Roversalmost had the lead through Savage, who was back from suspension. He fired just wide of Jose Reina's goal on 25-minutes.
Confusion reigned on 33 minutes when Liverpool were initially awarded a penalty for a foul on Cisse by Khizanishvili after the Frenchman was set clear by the improving Bolo Zenden.
Referee, Mark Halsey was overruled by the assistant referee, who correctly asserted that the foul took place outside the box. Following the dismissal, Zenden hit the bar with the free-kick, but the sides went in at the break on level terms.
After the break Cisse continued to be Liverpool's chief threat, but the striker's opportunities would have been doubled for just taking a chance on the numerous knockdowns fed to him by the majestic Crouch.
But Rovers had understandably settled in deep for a point and Liverpool desperately needed a shot in the arm.
Cisse was doing his best to provide it. The Frenchman forced the first save out of ex-Anfield keeper Brad Friedel with yet another header with 25 minutes left on the clock as he tried to rouse the home fans. He missed another chance, this time with his feet, from Luis Garcia's cross, blasting wide from the edge of the edge of the box.
Fernando Morientes replaced Crouch in attack, making his first appearance in two months, but he did little to break the resolute Rovers rearguard.
Cisse finally had his goal on 75 minutes, and his celebration matched the ferocity of the finish. Blackburn fans, who had taunted the Frenchman throughout with chants of "Cisse, how's the leg" following the horrific break suffered at Ewood Park last season, were left with egg on their faces as he dances joyously in front of them.
Morientes squandered three simple chances to get his eye back in, towards the end, but the day belonged to Cisse. Liverpool were far from impressive, but a win was paramount.
Man of the Match: Djibril Cisse - A wonderful finish which capped a fine performance from the highly-strung Frenchman. In a season where Liverpool are struggling for goals with Cisse on the bench, starting he could have had five.