His arrival on the hour changed the course of a match which until that point, had been heading for a draw, despite the home side enjoying the better of the opening 45 minutes.
Malbranque tapped home after Shay Given had kept out Collins John's shot on 75 minutes to take the three points and exorcise the memory of last week's FA Cup defeat to Leyton Orient.
Keeper Given kept his side in the game in the opening half with a string of saves - the first of which came after only seven minutes. The ball broke to Heidar Helguson in the penalty area and the striker's turn and shot nearly wrong-footed the Newcastle shot-stopper, but he stuck out a leg to clear the danger.
Given denied the home side for a second time just five minutes later, this time coming off his line to take the ball off the head of Brian McBride with the striker about to have a free header on goal.
And when the Irishman tipped over a long-range volley from Tomasz Radzinski, Fulham boss Chris Coleman must have been left wondering if it was his day.
The game threatened to boil over midway through the half and referee Alan Wiley wasted no time in showing the yellow card to Lee Clark. The Newcastle midfielder, returning to his former club, tripped Sylvain Legwinski, and when Stephen Carr went into the book for two challenges on Luis Boa Morte, the visitors looked rattled.
But they regained composure as the half wore on, with Nolberto Solano looking to break at every opportunity and Charles N'Zogbia seeing an effort saved by Antti Niemi, making his debut in the Fulham goal.
Alan Shearer, looking for a goal to break Newcastle's club scoring record, had little opportunity in the opening 45 minutes and ploughed a lone furrow as Graeme Souness opted for a five-man midfield.
The visitors came out strongly after the break as they pressurised the Fulham goal and N'Zogbia saw an effort from the edge of the box deflected wide by Ian Pearce, but it wasn't long before normal service was resumed at the other end of the pitch.
However, it wasn't until the 74th minute that Fulham finally ended the deadlock. McBride broke down the middle of the pitch and played in substitute John. The wide man saw his first-time effort saved by Given, but Malbranque followed up with a simple tap in.
Late in the game, McBride saw an effort rebound off the crossbar as Fulham completed a comfortable afternoon's work.