Although never coasting through Scott Parker's early second-half goal, Newcastle appeared to have enough left in the tank to secure their second win of the season.
But super-sub Wayne Routledge changed it around with two telling crosses.
First he set up Brian McBride's equaliser and then substitute Carlos Bocanegra's winner on the ground where he made his Fulham debut three seasons ago.
And it was no surprise that Newcastle were caught out twice in the last 10 minutes after the magnificent Parker had left the field through injury.
The one down side for Fulham was the loss of the inspirational Jimmy Bullard in the first half with a sickening injury.
In a challenge with Parker – who was vindicated by both managers – Bullard's studs caught in the turf resulting in his knee going in one direction and his leg the other.
Clearly in considerable pain, Bullard had his right leg strapped and was rushed straight to hospital with what appeared to be a dislocated knee-cap.
Parker was visibly upset by the incident – which was a complete accident – and took some time to gather his composure.
Fulham had started well with ironically, Bullard calling the shots in midfield.
Newcastle gradually took control and Damien Duff flashed a couple of efforts wide that Antti Niemi had covered.
Obafemi Martins struggled to get into the game and was off the pace while his shooting lacked direction.
The nearest Newcastle did come to breaking the first half deadlock came in the dying seconds when Stephen Carr's surging run ended with a shot that Niemi touched over the bar.
Newcastle lifted the tempo after the break and Martins was presented with an early opportunity on the edge of the box, but snatched at the ball and it flew wide.
Despite plenty of pressure a goal was looking elusive until Emre floated in a cross from the right and Liam Rosenior was caught ball-watching as Parker came in on the blindside to head in his second goal of the season.
That proved just the lift as Newcastle piled on the pressure and Niemi watched as a Charles N'Zogbia drive flew wide and he superbly saved from the same player.
Giuseppe Rossi went on for Martins after 70 minutes but had as little an impact as the Nigerian.
But the biggest turning point came on 81 minutes when Routledge took full advantage of a Peter Ramage slip and McBride drove in his cross at the back post from a tight angle.
Still reeling from that blow, Newcastle were counted out six minutes later.
Shay Given made an excellent save with his legs from Luis Boa Morte at the expense of a corner.
Routledge took the kick and McBride's headed crashed against the bar and was bundled over the line by a gleeful Bocanegra.
The jeers at the final whistle told their own story.