Portugal international Cristiano Ronaldo was once again a controversial figure and was loudly booed every time he touched the ball after a highly debatable penalty in the first half.
Middlesbrough players were furious when Ronaldo fell in the box after a challenge by goalkeeper Mark Schwarzer. The Australian did not appear to make any contact on Ronaldo but referee Chris Foy pointed to the spot.
The Middlesbrough players surrounded the Merseyside official and vented their anger over a highly debatable decision which gave Louis Saha a chance to redeem himself after missing a penalty against Celtic in the Champions League last month.
The former Fulham player made no mistake with a left-foot shot to the right of Schwarzer. The goalkeeper flung himself across goal but failed to get a hand on the ball.
Middlesbrough put up a brave fight and levelled in the second half only for United to hit back immediately for the match-winning goal.
Boro boss Gareth Southgate recalled home-grown Stewart Downing after injury against a United side eager to maintain an unbeaten away record in the league this season.
United star Paul Scholes was booked early in the game for a foul on Lee Cattermole.
Middlesbrough, who have often been criticised for a negative approach, were enterprising from the kick-off in their thirst for an early goal.
However, Former Chelsea defender Robert Huth came to the home side's rescue in the 12th minute when he cleared a Saha header off the line.
Shortly afterwards Ronaldo fired in a powerful shot which was parried by Schwarzer but Ryan Giggs headed the follow up wide.
Immediately after Saha's penalty, Middlesbrough were unlucky when Abel Xavier headed against a post with Edwin Van der Sar beaten. Huth then followed that up with a long-range shot that was wide of target.
Malcolm Christie, making his first home appearance for a long time following injury, was booked for a foul on Scholes before Wayne Rooney steered a shot just wide from a left-wing pass by Ronaldo.
Middlesbrough sent on substitute James Morrison for the injured Jonathan Woodgate immediately after the break.
Morrison, one of the many products from Middlesbrough's highly rated academy, sent the home crowd into raptures when he levelled the scores with a volley from the right after 66 minutes. The Darlington teenager was mobbed by his team-mates at the corner flag.
However, their joy was short lived as Darren Fletcher scored with a header from a left-wing cross by Giggs just two minutes later to settle the match.