For the third year running the Addicks went out at the fourth round stage in the FA Cup, despite looking anything like 3-0 losers at half time.
Two very even sides cancelled each other out in the first 45 minutes - and if anything Charlton had the better chances.
Keeper Maik Taylor did brilliantly to get down and save a point blank header from Luke Young as the defender connected with a cross from Jonatan Johansson on 36 minutes.
Four minutes later Taylor could only parry a Young cross straight to Richard Rufus but the half chance was squandered when Rufus volleyed over from just seven yards.
For all that, Fulham exerted the most pressure but were reduced to long-range shots with Sean Davis almost through on 23 minutes. The Cottagers midfielder was nudged off the ball at the last second by Jason Euell and the effort trickled into the arms of Dean Kiely.
If the first half was tame stuff the second period sprang into life once Malbranque scored.
For the first time the well marshalled Charlton defence opened up to allow Luis Boa Morte to cut across from left to right before passing outside to Malbranque who took his time before planting a rising right foot shot high into the net.
Johansson then attempted an audacious overhead volley but Charlton knew it wasn't their day when Scott Parker's chip was headed down by Shaun Bartlett only for Taylor to pull off another top drawer save.
Young who had already been booked then clipped Boa Morte just inside the box and Malbranque's penalty sent Kiely the wrong way.
It got worse for the visitors when a Rufus back header was woefully short and Mark Fish's was even worse.
Facundo Sava got himself between the ball and Fish and the Charlton defender was reduced to dragging Sava down.
As the last man, Fish was left with the long walk back to the dressing room while Malbranque sealed his side's win by thumping his second spot kick straight down the middle.