The England captain, playing in central midfield, netted a first-half double on Boxing Day and delivered an exquisite pass for Robin van Persie to score United???s third, as Newcastle fell to their fourth defeat in a row in all competitions.
Papiss Cisse pulled one back from the spot late on for the visitors but Alan Pardew will rue the fact his side weren???t awarded a penalty when the game was goalless, as his team slip to 10th in the top flight.
However, his fragile defence – which has now conceded 12 in their last four – was opened up with ease by a United side which has won seven of their last eight matches and sit ten points adrift of Premier League leaders Chelsea.
United had won their last 10 Boxing Day fixtures going into the contest and Rooney came close to putting the hosts ahead with just three minutes on the clock when he headed Juan Mata???s chipped through ball goalwards, but was ruled offside.
Newcastle then showed their threat on the counter-attack when 17-year-old Adam Armstrong ??? making his first Premier League start ??? outmuscled Jonny Evans and hooked a cross in for Ayoze Perez, who was unable to connect with a scissor kick.
And just moments later the visitors could have been awarded a penalty-kick when Mata clipped the heels of Yoan Gouffran as he burst into the United box, but referee Mike Jones waved away Newcastle???s appeals.
Robin van Persie responded for the hosts, firing Rooney???s lofted pass into the side-netting after beating the offside trap, but Newcastle continued to pose United problems and Daryl Janmaat drew a fine save from David de Gea from 25 yards out.
However, it was United who made the decisive breakthrough on 23 minutes, when Radamel Falcao met Mata???s deep cross and squared for Rooney, who had surged forward from his central midfield role to convert a simple finish from six yards.
Falcao should have doubled United???s advantage moments later when he glanced Ashley Young???s superb in-swinging cross wide of the far post but Rooney was on target again with 36 minutes on the clock to put the Old Trafford outfit in complete control.
Falcao???s fierce tackle on Armstrong won the ball back for United and Mata slipped a simple pass through to the on-rushing and unmarked Rooney, who clipped in his eighth of the season from 12 yards.
Moussa Sissoko fired straight at De Gea from long range as Newcastle attempted to strike back, however, United went in at the break with a comfortable cushion and extended their lead just eight minutes after the re-start.
Again Rooney was involved, lofting an inch-perfect pass into the penalty box for the loosely-marked Van Persie to head into the corner for United???s third and his fifth in his last six Premier League appearances.
The Dutchman then looked set to add a fourth on 56 minutes but Newcastle scrambled the ball away, before Armstrong fired a half-volley wide from the edge of the box after Colback???s free-kick had been half-cleared by Rooney.
United were in full control of proceedings by the hour mark, though, and Jak Alnwick had to parry away a Rooney shot from the edge of the box after neat work from Van Persie and Falcao, before Rooney landed a 25-yard free-kick on the roof of the Newcastle net and Van Persie mis-timed a right-foot volley from 10 yards out.
Pardew threw Papiss Cisse and Remy Cabella on in search of a lifeline and Ayoze Perez nearly pulled one back on 79 minutes after skipping past Paddy McNair, but was unable to beat David de Gea at his near post from a tight angle.
United looked on course to register their fourth clean sheet in five home games but Phil Jones carelessly stuck out a leg and tripped Jack Colback in the box late on, allowing Cisse to fire a superb penalty into the top corner on 86 minutes.
The goal failed to spark a grandstand finish from Newcastle, though, and Louis van Gaal???s side saw out the remainder of the match to continue their excellent run of results.??