The Scot, who also netted the winner in the Blues' last triumph over United a decade ago, swooped to meet Mikel Arteta's free-kick in a hotly-tempered game which saw Gary Neville sent off for kicking the ball at Everton fans and Paul Scholes dismissed in stoppage time.
Everton hero-turned-heathen Wayne Rooney was once again the centre of attention. He joined Ruud van Nistelrooy, who ended his goal famine with a brace against Newcastle on Sunday, in attack.
Toffees boss David Moyes resisted the temptation to place sixteen-year-old James Vaughan against Rooney in a battle of the teenagers, choosing instead to leave him on the bench.
Misfiring record signing James Beattie also had to be content with a place in the dugout after recovering from a knee injury. Alan Stubbs was missing with a dislocated shoulder.
A fervent Everton crowd did their utmost to unsettle the seasoned United stars, creating a wall of noise around Goodison, which has been so lacking this season despite a fine league campaign.
Rooney, who took the brunt of the abuse, and the brunt of a nosebleed-inducing arm in the face, came close to ramming the taunts down his former fans throats with a magnificent strike from distance on seven minutes, which Nigel Martyn struggled to parry.
Everton, looking for their first win against Sir Alex's Ferguson in 20 league games, matched United's high-tempo breaks early on, but rarely looked likely to penetrate Wes Brown and Rio Ferdinand's high-quality resistance.
United expertly took the pace out of the game and the decibels out of the stands, as they had expertly done in the FA Cup tie.
But Everton, as they have done all season, doggedly fought on and regained the initiative and almost had the lead ten minutes before the break. A Ferguson header needed Roy Keane's intervention off the line before Arteta's spectacular effort was again repelled from the goal-line, this time by Ferdinand.
Marcus Bent's woeful finishing denied the Blues another chance to gain the lead before the break with a header that hit his shoulder, followed by a wayward volley which span high over the bar.
United's first clear opportunity came four minutes after the interval when the ever-inspirational Rooney chipped a perfectly weighted pass over Joseph Yobo's head into the path of Scholes, whose effort was brilliantly saved by Martyn.
After winning an intense five-minute midfield battle, Everton had the lead. Arteta's beautifully flighted free-kick, found Ferguson unmarked in the six-yard box. The Scot swooped in trademark fashion to send the Goodison faithful into a state of delirium.
United rallied, and although Ronaldo teased and cavorted and Scholes blasted just over, there appeared to be little way back into the game for Sir Alex Ferguson's shell-shocked side.
Ronaldo finally added a little productivity to his posturing on 70 minutes when he stung Martyn's fingertips from distance, but van Nistelrooy, was unable to convert the rebound under pressure from Yobo.
Neville inexplicably got himself sent off 18 minutes from time as United tempers frayed. The England full-back responded to taunts from the Everton fans by booting the ball into crowd. Referee Phil Dowd had no hesitation in brandishing the red card.
As news of Liverpool's away win at Portsmouth filtered through, it was all the more important that Everton held on to this triumph and they showed no sign of faltering.
Tony Hibbert cleared off the line from Ferdinand and van Nistelrooy missed his kick with the goal at his mercy, before Scholes saw red for his second booking after a terrible lunge on Kevin Kilbane.