The match was even throughout and both sides produced an entertaining contest despite a 0-0 scoreline after 120 minutes.
Brazilian youngster Anderson scored the decisive penalty in a 4-1 shoot-out win for the quadruple-chasing champions.
The first half was largely Tottenham's. Despite a bright start from the Premier League leaders, it was largely the initiative from Aaron Lennon and Luka Modric which looked likely to break the deadlock at Wembley.
Early pressure from United saw Cristiano Ronaldo go close twice, firstly from a trademark free-kick which went narrowly over, before the Portuguese winger had a shot from within the area which was saved by Heurelho Gomes.
The only other first-half efforts from Sir Alex Ferguson's side came from distance as the makeshift Spurs defence held firm after a nervy opening ten minutes.
Young midfielder Darron Gibson unleashes a venomous shot which flew just over the bar and on 25 minutes, Rio Ferdinand controlled a bouncing ball beautifully to hit a dipping half-volley which had Gomes worried.
After that it was all Tottenham. Lennon repeatedly beat his marker on the right-hand side but he could not find a cross to find the Spurs frontmen.
In all fairness to Lennon, while Darren Bent toiled endlessly, Roman Pavlyuchenko was having a nightmare afternoon, resulting in being dragged off after an hour.
The second half produced more of the same from Spurs. Both sides applied pressure at different times throughout the second 45 minutes, but it was the likes of Jonny Evans, Ferdinand, Ledley King and Michael Dawson who were on top.
The first clear-cut chance fell to Lennon after Benoit Assou-Ekotto picked him out on the edge of the area. He powered a shot to the right of keeper Ben Foster, who saved well.
It wasn't until right at the death that United threatened to score. The quick feet of world-player-of-the-year Cristiano Ronaldo took him inside the penalty area to lash a shot past Gomes. It crashed against the near post and gave Spurs a huge let-off.
As legs got heavier throughout extra-time, the pace of the game dwindled. A chance for Bent was stopped by the legs of Foster, while Patrice Evra flashed a shot over the bar in the last minute.
To extra-time it went and missed spot-kicks from substitutes David Bentley and Jamie O'Hara cost Tottenham the chance to retain the Carling Cup, as Anderson slide home his side's fourth penalty to secure the silverware.