Best, standing in for the injured Shola Ameobi and responded with a second-half double to earn Newcastle the three points.
However, the Magpies were indebted to Tim Krul for three superb second-half saves from Steve Sidwell, Chris Baird and Danny Murphy before he was finally beaten for the first time in the new Premier League campaign by Clint Dempsey's 88th-minute header.
It was far from a vintage performance by the home side, but just as they did at Sunderland last weekend, they got the job done to bank another precious three points.
After yet another eventful week at St James' Park during which Joey Barton's stand-off with the board came to a head and striker Nile Ranger was arrested, the club's fans voted with their feet, or at least a significant proportion of them did.
There were around 10,000 empty seats inside the stadium as the game kicked off, and while an attendance of 42,684 might be regarded as more than satisfactory at many clubs, the gaps on the terraces reflected the general level of dissatisfaction with the current state of play in the club's summer recruitment drive.
Matters were not helped by the injury to Ameobi which saw Pardew turn once again to Best and Peter Lovenkrands, and as Fulham dominated the early stages with the Magpies unable to compete in the middle of the field, the mounting frustration was almost tangible.
However, for all that the current squad may lack strength in depth, there is little shortage of courage and commitment and the fact that they were able to limit the visitors to a single shot on target, a 12th-minute Pajtim Kasami effort which was easily claimed by Krul, brought some comfort.
Newcastle were disjointed in the middle of the field and it was not until Cheick Tiote, who is gradually shaking off the after-effects of an interrupted pre-season, managed to make his presence felt that the Magpies began to push the Londoners back.
Pardew's side still struggled to create anything of note until the game exploded into life with the half-time whistle fast-approaching.
Winger Jonas Gutierrez forced Mark Schwarzer into his first save of the half with a 44th-minute header, and that was the cue for the home side to make a late push.
Former Magpie Aaron Hughes got in a vital block to deny Best after he had turned smartly inside the box, and Schwarzer had to tip a curling Yohan Cabaye effort over his crossbar.
From the resulting corner, the ball dropped to last weekend's derby hero Ryan Taylor, and his shot from 20 yards flew inches past the far post with the Fulham keeper stranded.
Newcastle returned with their momentum intact and forced their way in front within three minutes of the restart.
Schwarzer could only palm Cabaye's shot onto the crossbar after it had bounced nastily in front of him and Best when in the right place at the right time to tap home.
The lead might have been short-lived had Krul not been at his best with 56 minutes gone.
Damien Duff and Baird exchanged passes on the right before the winger sent in a cross which Steve Sidwell headed powerfully towards goal, only for the Dutchman to turn his effort onto the bar and enjoy better fortune than his opposite number as the ball went out for a corner.
Dempsey fired just wide from a tight angle and Duff blasted into the side netting with Fulham searching desperately for a way back into the game.
However, their hopes were dashed with 66 minutes gone when substitute Demba Ba controlled Gabriel Obertan's inviting pass and cross for Best to turn smartly inside the area and fire past Schwarzer.
Krul pulled off fine saves to deny first Baird and then Murphy as the Magpies fought stubbornly to protect their clean sheet.
But they found themselves under pressure once again as they conceded a series of late free-kicks, and their defences were finally pierced from one of them with two minutes remaining when Dempsey headed him from Murphy's cross.
Schwarzer tipped an injury-time piledriver from Ba onto the woodwork, but there was no way back for his side.