Goals from Collins John and Luis Boa Morte, together with a fine display from substitute keeper Tony Warner, sealed an emotional win and left Fulham fans on a high.
Fulham were desperate to grace the memory Haynes, who died at the age of 71 following a car crash this week.
The former England captain was known as The Maestro at Craven Cottage, where he played 658 games between 1952 and 1970, scoring 158 goals.
And he would have enjoyed an amazing afternoon in which Collins John put Fulham ahead and Boa Morte sealed three points with a superb second - leaving Fulham fans singing "Johnny Haynes' black and white army".
But it was keeper Warner, who was born in Liverpool and was on their books from 1990 to 1999, who also played his part. He came on for injured Mark Crossley after 63 minutes and made four superb saves to earn Fulham the points.
Haynes was renowned for his wonderful passing and regarded as Fulham's greatest ever son and there was an emotional one-minute's silence in his memory before kick-off.
Many experts have described Haynes as the David Beckham of his day, such was his profile in the 1950s when he led his country and was one of original 'Brylcream boys'.
His former team-mate Tosh Chamberlain helped fans lay a wreath on the pitch before kick-off and in the match day programme England 1966 hero George Cohen described him as "the best player I have ever played with". Some compliment from a man who won the World Cup for England!
It was always going to be an emotional day for Fulham and the home team began like they meant to honour Haynes' memory in style.
In fact, they could have been ahead as early as the second minute when John broke through two challenges in the penalty box and passed left to Steed Malbranque.
The winger's cross fell perfectly for Ahmad Elrich, on his full league debut. But with keeper Jose Reina already out of the picture the Australian somehow scooped his effort over the bar.
It turned into rather a scrappy half after that, but Fulham had the better of it and Liverpool, with Harry Kewell handed his first start of the season, looked toothless.
Rafa Benitez's men were missing the drive of captain Steven Gerrard in midfield and Fulham made them pay after 30 minutes.
Claus Jensen received the ball on the edge of the area and chipped a perfect pass through for John - who was marginally onside. The Dutchman took it on his chest and stroked a sweet shot home to Reina's left.
It was no more than Fulham deserved and Liverpool rarely threatened at the other end of the pitch.
They were finding John a real handful and with Fulham captain Boa Morte working tirelessly in a new central midfield role, the home side held all the aces.
Liverpool, in fact, were awful. Memories of the midweek Champions League victory in Anderlecht were soon forgotten as they stumbled their way through the first half without even putting two passes together.
The biggest surprise in the second half was that Liverpool manager Benitez didn't make changes. He chose to stick the same team that had been so miserable in the opening 45 minutes and nothing much changed.
Fulham enjoyed a good spell of pressure after the break and Josemi was booked for a terrible foul on the ever-dangerous John.
Then when Liverpool had a rare chance on the break after 56 minutes Djibril Cisse completely wasted it by directing his low cross straight to a Fulham defender.
Benitez reacted by bringing on Luis Garcia after 58 minutes and he almost made an immediate impact but saw his cross just cut out by keeper Matt Crossley.
That was Crossley's last action of the game because he suffered a recurrence of a groin injury after 63 minutes and had to be replaced by Warner.
The new boy kept Fulham in it with four fine saves. First he tipped a Fernando Morientes lob over the bar and then he spectacularly dived to his right to somehow keep out a curling effort from Garcia.
Then, as Liverpool desperately tried to grab equaliser, he dropped low to keep out a fiercely-driven effort from Sami Hyypia after 76 minutes and finally flung himself to keep out a near-post shot from Cisse.
In the end Fulham were worthy winners and they sealed victory in the dying minutes when Malbranque cleverly put Boa Morte through and he scored a second with a superb left-foot shot.
Man of the Match: Collins John - The young Dutch striker made it three goals in three games and set the Cottagers on their way to a crucial victory.