Mourinho was forced to watch the closing stages of the Carling Cup final from a TV gantry after being sent off by referee Steve Bennett.
The former FC Porto manager appeared to goad the Liverpool fans following his side's equaliser.
However, the game was about a remarkable Chelsea comeback after they had gone behind to a first minute strike from John Arne Riise.
The Norwegian rammed home a brilliant left-footed volley past the dive of Chelsea keeper Petr Cech.
The Blues, rocked by the early strike, took some time to recover their composure, but they stuck to their task of retaining the ball and gradually took control of the game.
In the 28th minute Didier Drogba had an excellent chance to level the scores. But after picking up a Joe Cole pass, the Ivory Coast striker could only poke the ball towards goal and Jerzy Dudek saved easily.
Mourinho subbed the ineffective Jiri Jarosik for striker Eidur Gudjohnsen at half-time. The change spurred Chelsea on and they levelled the final with 12 minutes left.
The goal owed much to good fortune as Paulo Ferreira's right-footed free-kick skimmed off the head of Liverpool skipper Steven Gerrard past Dudek, and into the net off the keeper's left upright.
Chelsea deserved to take the game into extra time and they quickly powered into a 3-1 lead.
With 18 minutes of extra time played, Drogba poked Chelsea ahead for the first time.
A long throw from substitute Glen Johnson caused panic in the Liverpool penalty area, and the striker stabbed the ball over the line.
Liverpool's heads went down for the first time and four minutes later Chelsea scored their third.
Mateja Kezman, a cult figure for the Blues faithful more for his effort than his goalscoring, repaid their faith in him.
Liverpool were unstuck by a byline drive from Gudjohnsen and up popped Kezman at the near post to bundle the ball over the line.
A lack of concentration from Chelsea allowed Liverpool to get back into the game almost immediately. Cech failed to grab a left-wing cross and the ball bounced off Antonio Nunez's head and over the line.
A frantic last-gasp finish by Liverpool almost paid off when substitute Igor Biscan powered a downward header on target but Cech scooped the ball into his arms.
But Chelsea were deserved winners as they ended a disappointing week on a high.