Forty-three places separate League One leaders Leeds from the Red Devils, but it would have been difficult to tell which team was which in this feisty Old Trafford encounter.
Leeds hassled United throughout and the home side never recovered from the shock of going behind to Beckford's 19th minute strike.
The combative Jonny Howson won the ball on the right inside the Leeds half and his long raking pass sent Beckford racing away into United territory.
Beckford fought off the attention of United defender Wes Brown and capitalised on the hesitancy of goalkeeper Tomasz Kuszczak to roll the ball beyond the Pole and into the net from ten yards on the left side of the box.
This is the first time United have been knocked out of the FA Cup in the third round since a 2-0 defeat at Bournemouth 26 years ago.
The result saw the first time that a Sir Alex Ferguson United team have lost to a lower division side in the competition.
United were lethargic in their approach with only Wayne Rooney approaching true form.
He had United's best chance of the game in the 25th minute after Dimitar Berbatov had sent the England striker racing away down the right.
Leeds goalkeeper Casper Ankergren came off his line to meet Rooney's shot from 12 yards which hit the underside of the Dane's body and looked to be heading for the back of the net until Jason Crowe's superb goal-line clearance saved the day.
The Red Devils had a number of half chances, but Leeds were terrier-like in their ability to get bodies and boots in the way of the ball.
In fact the clearest cut chances fell to the visitors.
In the closing minutes, Beckford was inches away from a second goal with a shot from the edge of the United penalty area, while substitute Robert Snodgrass saw a fierce 25-yard free-kick rattle the crossbar.
Not even five minutes of injury time could rescue the home side from this shambles of a performance and, on this form, it will not be long before the two sides are meeting again in the Premier League.