Ivan Cavaleiro hit the winner with a beautiful curling effort 10 minutes from time to sink the struggling Yorkshiremen.
Karlan Grant's third goal of the campaign had earlier cancelled out Aleksandar Mitrovic's opener.
Calls for Siewert to be sacked had grown earlier in the week after the Terriers were dumped out of the Carabao Cup at the hands of Lincoln.
The under-fire German has won just one match as manager, with relegated Huddersfield failing to win a game since February.
The Terriers enjoyed the best of the first half but once again their goal-shy attack, which has scored just seven times from open play in 18 games under Siewert, failed to deliver.
Steven Sessegnon, who was making his league debut for Fulham, produced a brilliant lunging block to keep out Lewis O'Brien's third minute effort as Huddersfield started quickly.
Alex Pritchard flashed a long range effort wide on seven minutes as the Terriers continued to look positive.
Cavaleiro sent a curing effort wide a minute later after Kamil Grabara flapped at a cross.
The forward then scuffed an effort straight at Grabara on 18 minutes following a surging run into the danger zone.
Terence Kongolo headed wide from a 28th minute corner, before Pritchard won another corner a minute later as Huddersfield kept up the pressure.
It led to increased frustration among the home fans as possession was squandered in key areas in the run up to half-time.
Grabara got down well to keep out Joe Bryan's fierce shot across goal on 41 minutes during a rare Fulham attack.
Mitrovic blazed over at the start of the second half after his initial shot had been blocked by Christopher Schindler.
Grabara turned an Anthony Knockaert shot away with his legs as the visitors started to turn the screw.
And they got their reward when Mitrovic beat Tommy Elphick at the back post to head home on 51 minutes after Juninho Bacuna had initially made a mess of a clearance.
But the lead lasted just six minutes when Grant got his third of the season after his header hit the post and was ruled by goal-line technology to have crossed the line.
Grabara got the better of Knockaert in a one-on-one on 60 minutes as the game began to open up.
And the Cottagers wrapped it up late on when Cavaleiro curled into the top corner after he had been given far too much space on the corner of the box.