Michael Carrick gave Sir Alex Ferguson's side an early lead with a scrambled effort, before a second half penalty from Robin van Persie effectively sealed the three points.
Despite Manchester City's derby win last week, the gap between the two teams at the summit of the table is surely too great to overcome.
Here are the player ratings for the Red Devils on a satisfying afternoon.
David de Gea: 7
Another game, another consistent performance from the once maligned Spaniard.
David de Gea was kept mostly untroubled in the first half, but made several stops in the second to deny the Potters a route back into the game.
Phil Jones: 6
Manchester United's man for every position was defensively solid against Jonathan Walters down the right flank, rarely getting caught out by the converted wide man.
Going forward he was far less influential, his link up play with Antonio Valencia bordering on the embarrassing at times.
Nemanja Vidic: 8
Captain of the Red Devils, Nemanja Vidic played like it Sunday afternoon.
The Serbian beast was completely dominant in the air, keeping Kenwyne Jones stifled for the best part of the game. He has been one of the side's most reliable players in 2013.
Rio Ferdinand: 6
A composed, if unspectacular game at the back for the United veteran.
With Vidic keeping Jones nicely under wraps, Rio didn't have much to do as the majority of Stoke's attacks came from out wide.
The England international was wholly comfortable dealing with these crosses.
Patrice Evra: 6
Patrice Evra has had a couple of real stinkers in United's last couple of games, but bounced back well against Stoke.
The Frenchman was beaten by Ryan Shotton a couple times though, and was perhaps lucky his opponent lacked a decent end product.
Michael Carrick: 7
Unpretentious but effective, Michael Carrick was key to Manchester United's midfield dominance in the first half.
His goal may not have looked pretty, but a player like him will surely take anything he can get in this department.
Wayne Rooney: 8
Quite possibly the Red Devils' best player and a real revelation in the box-to-box role.
United have lacked a controlled, physical presence in midfield this season, which begs the question—why hasn't he been used like this before now?
Shinji Kagawa: 7
The Japanese playmaker's passing wasn't perfect Sunday, but he was a positive influence in the final third of a congested pitch.
Kagawa darted back and forth, providing space for himself and teammates and holding the ball up well in tight situations.
Antonio Valencia: 3
One feels like sighing every time Antonio Valencia's name is brought up at the moment.
He was borderline-atrocious against Stoke, failing to beat the average Geoff Cameron once on the dribble and looking generally impotent in attack.
Javier Hernandez: 6
Lots of huff and puff for the clinical forward, but he received little in the way of service from his teammates.
Perhaps the biggest plus for the Mexican was his willingness to throw himself around physically against a side regarded as the rugby team of the Premier League.
Robin van Persie: 7
How relieved did Robin van Persie look when his neatly-taken penalty evaded the diving Asmir Begovic?
The Dutchman's ecstatic celebration was a release of all the pent-up frustration that has been building during his six hour-plus scoreless run.
Danny Welbeck: N/A
A late replacement for Javier Hernandez, Welbeck had too little time to make an impact on the game.
Who impressed you most in Sunday's game? Should Antonio Valencia consider a career-change?