The United skipper was left out by boss Fergie after the England defender appeared to swear at him during amazing scenes in United's Champions League game against Lille in Lens last week.
Neville became embroiled with Lille players on the touchline as the French team walked off in protest after Ryan Giggs' controversial late winner.
Ferguson could be seen hurrying to the touchline to tell Neville to back away and leave the French players to their own devices.
In the heated exchange between the pair, Neville could be clearly seen swearing at the 65-year-old Scot, who looked livid.
Grim-faced Neville could be seen talking on his mobile phone while his team-mates warmed-up, but Ferguson tried to laugh off the defender's absence.
He said: "I thought Fulham were going to play six of their big tall players so I opted to play Wes Brown.
"But when I saw the Fulham team-sheet they'd only played three of them - I got that one wrong, didn't I?"
Ferguson is likely to stick with Brown for Tuesday's FA Cup replay at Reading. An Old Trafford source said last night:
"The manager wasn't happy with what happened in Lille, so maybe he's just making it clear exactly who's in charge."