A week after his shock retirement U-turn, Scholes scored his first Premier League goal since August 2010 and his first goal at Old Trafford for almost two years when he turned home Wayne Rooney's cross-shot in first-half stoppage time.
It was the 151st goal of the 37-year-old's career and was more remarkable because Ferguson had told him to sit in the centre of midfield and control the play.
"It was a surprise to see him at the far post," said Ferguson.
"With his age and the fact he has just come back, we were looking for him to control central midfield, which he did.
"But he has the instinct. He always has had. He probably said 'it was nearly half-time, I will gamble'.
"He is one of our greatest players. When you see his performance today, you don't lose that."
Up to that point, it had been a struggle for United, who ran out 3-0 winners.
Wayne Rooney had a 20th-minute penalty saved by Adam Bogdan, who also repelled a couple of efforts from Danny Welbeck.
There were more nervy moments after the break but eventually Welbeck and Michael Carrick struck late on to allow United to move level on points with leaders Manchester City, who head to bottom club Wigan on Monday.
However, Ferguson was more vexed by the failure of referee Peter Walton to send Zat Knight off when he brought Welbeck down for Rooney's penalty.
It seemed like a clear goalscoring opportunity and at the end of a week when Vincent Kompany was sent off against United for a two-footed tackle but Glen Johnson stayed on for a similar offence on Joleon Lescott three days later, Ferguson feels it is time for some clarification.
"We should have been playing against 10 men," said the United boss.
"But these inconsistencies are confusing to everyone. Referees have to be given direction about what are the laws of the game and what should be permitted in terms of tackles.
"(Referees' chief) Mike Riley has to be given the rope to say this is not allowed, two-footed tackles are not acceptable, whether you take the ball or not.
"If he does that it would clarify the situation for all players, the referees and the fans."
Ferguson confirmed Welbeck had gone off with a twisted knee but should be fit for next Sunday's trip to Arsenal.
Bolton boss Owen Coyle admitted Scholes' goal had made for a great story, although not for him.
And, after outlining the timescale of Gary Cahill's departure for Chelsea, Coyle confirmed the move to get United States defender Tim Ream in from New York Red Bulls is at an advanced stage and the player was in attendance this afternoon.
"Do you ever want to lose a player of Gary Cahill's quality? No," said Coyle.
"But circumstances have brought it about and we wish him well.
"He is an outstanding player and an outstanding young man.
"Hopefully I can bring someone in, which we are very close to doing.
"We had Tim Ream in for a week and we would like him. We are close but we need to get an application in for a work permit so we don't want to get ahead of ourselves.
"We want to be respectful to the MLS but we are trying to bring it to fruition."