That result looked unlikely as United again showing signs of tiredness in an indifferent display until 17-year-old Macheda made his decisive contribution.
With one eye on next Wednesday's Champions League quarter-final second-leg tie against Porto, Manchester United manager Sir Alex Ferguson rested keeper Edwin Van der Sar, left-back Patrice Evra and winger Cristiano Ronaldo.
We gave it our all - Sbragia
There was also no Rio Ferdinand because of injury but Jonny Evans passed a late fitness test and partnered Nemanja Vidic in the centre of defence, while striker Dimitar Berbatov was handed a shock start despite pre-match reports of an ankle problem.
Wayne Rooney started on the left with Carlos Tevez partnering Berbatov up front and United predictably dominated early possession against opponents who relied on strike duo Djibril Cisse and Jones to provide them with an outlet.
It took United until the 15th minute to create the first real chance but Danny Collins superbly cleared Vidic's header off the line from Rooney's inswinging corner.
However, United were in front under a minute later as Rooney was afforded far too much time and space on the left flank and curled in a teasing right-footed cross which found Scholes, who looped a near-post header over Gordon for the opener.
Paul Scholes celebrates his first-half goal
Calum Davenport had Sunderland's best chance with the former West Ham man sending Phil Bardsley's cross just past the post.
Bardsley was causing problems down United's right and Jones, under pressure from Gary Neville, was just wide from one of his teasing crosses as Sunderland edged close to an equaliser.
Moments later Cisse forced a smart save from Ben Foster and as Sunderland continued to press, Evans almost turned a Carlos Edwards cross into his own net but the post spared his blushes.
Just before the break Park Ji-Sung fired just past the angle as United finished an indifferent first-half performance on a positive note.
Following the re-start, Rooney sent a fierce shot inches wide but it was Sunderland who were the next to celebrate as Tainio beat Park down the left and sent in a teasing cross which Foster fumbled into the path of Jones, who bundled the ball home from close range.
The goal seemed to galvanise United and Scholes was unlucky to see a half-volley fizz just wide of Gordon's post.
Half-chances for Tevez and Berbatov followed with Sunderland relying on the counter-attack and Ronaldo was introduced with 20 minutes remaining as United desperately sought inspiration.
We battled hard for win - Phelan
But it was another substitute, Macheda, who made the required impact just seconds after coming on by redirecting Michael Carrick's wayward shot into the corner of the net with a deft left-foot flick.
Victory sent United top with seven games left while Sunderland slipped closer towards the relegation zone with the Black Cats just two points off the bottom three.
Sunderland manager Ricky Sbragia:
"They haven't done it for the last three or four games, but today I thought they were excellent.
"It is always a cruel blow when you're 1-1 with Man United. Not sure how much Macheda knew about (the goal) but he's in a rich vein of form so that's how it goes.
"We had our chances and if we had been a bit more ruthless we could have been 2-1 up at half time.
"The next six games are going to be really difficult and really hard. There are going to be a lot of changes here, there and everywhere regarding the table."
Manchester United boss Sir Alex Ferguson:
"Macheda has got something special about him, the boy. He side-footed it as it came to him. It's that quick-thinking that goalscorers have got.
"He wasn't fazed by anything. Right away, he got involved in the game and he had a good 20 minutes for us.
"The important thing is we have seven games left now and at this point, it is about cutting each game off as they come along.
"Today was an important away victory for us and we can be pleased with that."
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