Joe Cole came off the bench to keep Chelsea in touch with leaders Arsenal.
Cole replaced Didier Drogba late in the first-half and on 64 minutes he flicked the ball past Chris Kirkland from Frank Lampard's inswinging free-kick.
Dynamic Cole also hit the side-netting and another of his shots saw Harry Kewell head off the line.
Lampard had Chelsea's best chances in the opening period, going close with a shot, a header and also nearly connecting with a Damien Duff cross.
Before Cole's arrival, Rafael Benitez's deployment of five men in midfield had disturbed the fluidity of Chelsea's attacks and Jose Mourinho's side struggled to get behind the Liverpool defence.
Cole's introduction served to give Chelsea parity in midfield and almost brought some much-needed variation to their attack.
Benitez had made five changes to the side that lost against Olympiakos in the Champions League in midweek, bringing in Kirkland for his first start of the season and surprisingly including Salif Diao and Djimi Traore.
Liverpool contained Chelsea for long periods but in attack, with Cisse the lone striker, Benitez's side were painfully ineffective.
So much so that Petr Cech's only save of the game came in stoppage time when he fisted away Steve Finnan's shot.
The injury-plagued Kirkland had an uncomfortable start and was soon writhing in agony after he and Jamie Carragher tried to close down a Duff run.
The Liverpool goalkeeper had another nervy moment when he rushed to challenge Drogba at the edge of his box.
Soon after Cole's introduction, Paulo Ferreira got past Traore and picked out Lampard, whose header went well wide.
Lampard, who had earlier gone close with a low shot, then got on the end of Duff's cross from the left but he was unable to get enough of a touch on the ball to turn it into the net.
When Liverpool did get forward they were only able to create half-chances.
Cisse flashed a header past the post from a Harry Kewell cross and the Liverpool striker went even closer after a run and a shot that had Cech scrambling across his line.
Xabi Alonso also almost found Luis Garcia with a raking free-kick.
Five minutes after the restart Cole managed to get ahead of Carragher but his shot hit the side-netting.
Cole soon went even closer when from a Chelsea corner he fired in a shot.
Kirkland managed to get his hands to the shot but the Liverpool goalkeeper was grateful to Kewell, who headed the ball off the line.
Cole's persistence finally paid off when he got ahead of his marker and applied the most delicate of touches to Lampard's free-kick to give Chelsea the lead and ultimately the three points.
Chelsea: Cech, Paulo Ferreira, Terry, Ricardo Carvalho, Gallas,
Makelele, Smertin (Tiago 85), Lampard, Duff (Geremi 81),
Drogba (Cole 38), Gudjohnsen.
Subs Not Used: Cudicini, Huth.
Goals: Cole 64.
Liverpool: Kirkland, Josemi (Baros 71), Hyypia, Carragher,
Traore, Alonso, Diao (Hamann 78), Riise, Kewell,
Luis Garcia (Finnan 78), Cisse.
Subs Not Used: Dudek, Warnock.
Ref: P Dowd (Staffordshire).