Hughes will oversee his first home game since becoming Cottagers manager when Manchester United visit west London on Sunday.
Ferguson sold Hughes to Chelsea in 1995 and the former Wales striker believes the emergence of Scholes, who remains a class act at 35, was the catalyst for his departure.
"I could see Paul's quality back then and I think he hastened my exit!" he said.
"I left at the same time as Paul Ince and Andrei Kanchelskis because Alex had complete faith in the young players like Scholes, David Beckham and Nicky Butt.
"They were the future and I was the past. Sir Alex always was and still is very good at making key decisions at the right time. He got that one right."
Hughes expects Ferguson to arrive at Craven Cottage intent on reminding a player he managed for seven years of the pecking order.
"I've never come up against a weakened Man Utd team and maybe he likes his former players to know our place!" he said.
"He's always competitive but has a lot of affection for guys who have played for him and taken the next step through to management.
"He's always supportive but always likes to beat you.
"My relationship with him now is probably better than when I was a player.
"As a player I was grateful he allowed me to play in his team and that was it, but now I'm a manager we're closer."
Hughes remains thankful to Ferguson for his support after he was dismissed by Manchester City last December and knows he can turn to him for advice.
"Alex's words were very gratefully received. I've never been one of his ex-players who have sought a lot of advice from him," he said.
"I've had key conversations and that was obviously one of them.
"There's a pool of knowledge there that I can tap into if I ever need to.
"I haven't done that in recent times but that's not through lack of respect for what he can offer. I just haven't felt the need to.
"Certainly the fact he was on the phone very soon after the Man City situation is something I'm conscious of and something I was very grateful for at the time."