Spurs had taken a 24th minute lead through Robbie Keane and, although Carlos Tevez equalised 14 minutes later, the game turned on an incident midway through the second half.
United goalkeeper Edwin Van der Sar's long kick from the edge of the box landed perfectly for Wayne Rooney in the Tottenham penalty area.
With central defender Michael Dawson at his back, Rooney tried to turn the Spurs man.
The battle for possession looked to be going Rooney's way and Dawson threw out his arm across the United striker to handle the ball.
Referee Peter Walton had no option but to award United the penalty and show Dawson a straight red card.
Up stepped Cristiano Ronaldo and in tried and trusted fashion took a couple of steps, a shimmy and then drilled the spot-kick right footed into the bottom left corner of the net as goalkeeper Radek Cerny went the wrong way.
United sealed victory in the 88th minute when Ryan Giggs fed Ronaldo on the left corner of the Tottenham box and he took a couple of paces before scoring with a right-foot shot which crawled into the net under Cerny's body for his 25th goal of the season.
It was a harsh scoreline on Spurs and ended their hopes of a second Wembley final this season.
They had caused United numerous problems in an even first half and hit the Red Devils with a classic goal on the break to open the scoring.
Dawson's superb 50-yard cross-field pass found Aaron Lennon on the right.
The England winger skipped past left-back Patrice Evra with ease before his low cross into the centre was stabbed home by Keane from close range as he ghosted in between Wes Brown and Rio Ferdinand.
However, the chance of a first Old Trafford win for over 18 years was soon put into perspective when United equalised in the 38th minute.
Rooney's glorious long pass from the halfway line picked out Giggs on the left side of the Tottenham box.
He shielded the ball skilfully from Dawson before laying it off for Tevez, who scored with a crisp left-foot shot from ten yards.
Spurs had the chance to regain the lead seconds before the interval when Steed Malbranque's excellent through ball sent Jermaine Jenas racing clear.
His shot from just inside the United box was well tipped away one-handed by Van der Sar at full stretch.
Spurs came close with two other chances - one early and one late - to support their just claims for a White Hart Lane replay.
Dimitar Berbatov's 15th minute header from a Lennon corner was cleared off the line by Rooney's header and the Bulgarian saw a late flick from a Malbranque cross hit a post.
Tottenham must now content themselves with the Carling Cup Final, while the treble remains firmly in United's sights.