The news of Howard Kendall's death prior to kick-off led to a subdued atmosphere inside Goodison Park and the current crop of Everton players were unable to replicate the kind of performances seen under the club's greatest manager.
Non-existent marking from the hosts allowed Morgan Schneiderlin and Ander Herrera to put United 2-0 up inside 22 minutes and Rooney wrapped up the win in the second half.
The United captain has received criticism for his performances recently, but he looked like the Rooney of old, beating the offside trap and rolling the ball past Tim Howard to score at the home of his boyhood club for just the third time.
It was also his first league goal on the road since November last year.
All four corners of the ground took part in a minute's applause for Kendall, who oversaw Everton's most successful period in the mid-1980s, before kick-off.
A hushed atmosphere then descended upon Goodison Park
United looked nervous early on
Phil Jones, making his first start of the season, and Chris Smalling, were struggling to handle Romelu Lukaku.
The Belgian almost closed down David de Gea when he was sold short by two backpasses in the first six minutes.
The nervousness subsided in the 17th minute, when United took the lead
The hosts made it easy for the visitors
Herrera knocked the ball back to Juan Mata from a short corner Everton were not expecting
Steven Naismith's clearance fell to Marcos Rojo, who worked the ball to Schneiderlin via Chris Smalling's chest and he placed the ball into the far corner for his first United goal.
United were 2-0 up four minutes later, and again Everton's shoddy marking was to blame
Jon Moss played advantage after Seamus Coleman clattered into Anthony Martial and the ball fell to Rojo, who swung in a deep cross to find Herrera unmarked and he nodded in.
United played sensibly, keeping the ball rather than going for the jugular.
They seemed intent to play keep ball, but a clever run behind from Rooney gave them a chance to bag a third just before the break
The skipper squared to Martial, but he scuffed his shot.
Other than a fierce shot from Ross Barkley, which De Gea tipped over, Everton rarely threatened.
Roberto Martinez brought Arouna Kone on for Naismith at half-time and Van Gaal replaced Mata with Jesse Lingard.
The England Under-21 international made a telling impact, putting Barkley off his shot after he drifted into the box.
Everton looked more threatening with Kone and Lukaku up front
Rojo entered the book for taking down the Belgian and Bastian Schweinsteiger also saw yellow for pulling Barkley back.
De Gea then denied Lukaku a certain goal by saving with his left foot
Van Gaal was unhappy with his team and the referee
He argued with fourth official Robert Madley after a decision did not go United's way.
The Dutchman was sat happily clapping in his seat moments later, however thanks to Rooney's goal.
Schneiderlin received Phil Jagielka's wayward pass and nudged the ball to Herrera, who slipped Rooney in and he beat Howard to end a run of three successive defeats for United at Goodison Park.
TWEET OF THE MATCH
"Really cannot stress enough how bad Everton have been here
So bad Goodison seems to be more baffled than angry."
- Rory Smith @RorySmithTimes
https://twitter.com/RorySmithTimes/status/655407880020041728
PLAYER RATINGS
Everton
TIM HOWARD: 6
SEAMUS COLEMAN: 5
JOHN STONES: 4
PHIL JAGIELKA: 4
BRENDAN GALLOWAY: 6
GARETH BARRY: 6
JAMES McCARTHY: 6
AARON LENNON: 5
ROSS BARKLEY: 5
STEVEN NAISMITH: 4
ROMELU LUKAKU: 6
Substitutes
AROUNA KONE: 6
GERARD DEULOFEU: 5
Manchester United
DAVID DE GEA: 8
MATTEO DARMIAN: 6
CHRIS SMALLING: 6
PHIL JONES: 6
MARCOS ROJO: 6
BASTIAN SCHWEINSTEIGER: 8
MORGAN SCHNEIDERLIN: 7
ANDER HERRERA: 8
WAYNE ROONEY: 6
JUAN MATA: 5
ANTHONY MARTIAL: 6
Substitutes:
JESSE LINGARD: 6
MICHAEL CARRICK: 6
MAROUANE FELLAINI: 5
STAR PLAYER
Ander Herrera: Entrusted with the number 10 shirt and did not disappoint
The Spaniard scored his third goal of the season and played a part in the other two
Looked confident on the ball and his vision helped carve open the Everton defence.
MOMENT OF THE MATCH
Minute's applause for Howard Kendall: There is not usually much affection between Manchester United fans and their Merseyside counterparts, but the minute's applause for Everton's former boss was observed impeccably by the home and away fans.
VIEW FROM THE BENCH
Louis van Gaal showed his faith in Wayne Rooney by playing his captain up front and he did not disappoint
Van Gaal's decision to play Anthony Martial on the left against Seamus Coleman on his return from injury also caused Everton problems
Roberto Martinez made a mistake by starting Steven Naismith alongisde Romelu Lukaku
The hosts looked far more potent up front when Arouna Kone came on at the break.
MOAN OF THE MATCH
Phil Jagielka's performance
The 33-year-old, captained England on Monday, but looked remarkably average against Rooney
His sloppy pass allowed United to record their third.
NEXT UP:
Arsenal v Everton (Barclays Premier League, Saturday October 24)
CSKA Moscow v Manchester United (Champions League, Wednesday October 21)
Source : PA
Source: PA