Newcastle have struggled to recapture the form which saw them battling at the top of the table last season, and last night's win meant they have not recorded an away victory since last season.
"I'm worried in so much as we are not picking up enough points, that is pretty evident," he said.
"Although the performances against Stoke, Wigan and today have improved, it is a worry we don't have enough points on the board."
Fulham had been without a win in their last seven matches going into the encounter at Craven Cottage, before Steve Sidwell's shot in the 19th minute deflected off Mike Williamson and into the net.
It was their first goal in 317 minutes - and they could have had more were it not for a host of good saves from Newcastle goalkeeper Tim Krul.
Hatem Ben Arfa scored the equaliser for Newcastle ten minutes into the second half, his 22-yard shot curling in off the crossbar.
But soon afterwards Fulham restored their lead. Damien Duff floated in a cross from the right for Hugo Rodallega to head home, affording the London side the chance to sit back and look to hit Newcastle on the break.
Pardew was unimpressed by his side's defending which led to the winner.
"Second half we had the game by the scruff of the neck really, the goal was a soft goal," he said.
"We gave away a cheap free kick and then we didn't defend that situation well at all and have come away losing a game we should've got something out of.
"We just didn't defend it well it I'm honest, we are going to have to be better - we can't concede soft goals at this level. To win that game we needed to score three at Fulham and it is really difficult to do that.
"Of course it is very, very disappointing because I believe we have an honest set of players and we work on situations and really for us it is a poor goal, I can't so no more than that really."
Martin Jol praised the all-round influence of star striker Dimitar Berbatov, who controlled play for the side despite not getting on the scoresheet.
"I was happy that Berbatov, after talking to him, could fill in that role (behind the striker)," said the Fulham coach.
"It was vital, he didn't score so that was disappointing, but on the other hand he linked us up and kept the team together - I was very happy with him."
Berbatov's arrival was hailed as something of a coup for Jol and according to the Dutchman, both he and his squad are aware of how important the former Spurs striker is to Fulham.
"The good thing about my squad is that they realise Berbatov is an outstanding player," he said.
"For me the most important thing is that after losing (Clint) Dempsey - who is making the difference for Spurs now, as well as (Mousa) Dembele plus Danny Murphy and Bryan Ruiz (through injury) I'm very happy that he came to this club because otherwise maybe we could have ended up with a little problem."