Michael Carrick gave them a perfect start at the Britannia Stadium before Robin Van Persie ended his own personal goal drought with a second half penalty.
It was the ideal opening for United as Van Persie's corner was not cleared by Geoff Cameron and Carrick was on hand to scramble home his second goal of the campaign - poking his right-foot shot into the far corner.
The visitors came close to a second in similar circumstances as Patrice Evra fired over from another Van Persie delivery while Wayne Rooney, playing in a central midfield role, saw his effort well saved by Asmir Begovic.
Stoke were unusually troubled at defensive set-pieces and Carrick headed wide from Rooney's corner while an audacious Van Persie effort from 45 yards went well wide of its target in the blustery conditions.
United were first to create a chance in the second 45 minutes as Javier Hernandez played in Van Persie with a delicate pass, but the Dutchman shot into the side-netting from the angle.
However, United deservedly doubled their lead after 66 minutes when Van Persie was fouled by Andy Wilkinson in the area and Jon Moss immediately pointed to the spot.
The forward, who was without a goal since February before this game, ignored the wind, which had blown the ball off its spot, to fire low and hard to Begovic's left.
It was his 20th goal of the campaign and he sprinted down the touchline and headed straight for Sir Alex Ferguson. The manager lifted him up for a hug and then high-fived team-mates.
United now need only seven points from their remaining six games to ensure they cannot be caught by Manchester City and could win the title as early as next Monday night against Aston Villa.
Meanwhile, Stoke find themselves in real danger of slipping into the relegation zone, having won just once in 13 league games in 2013.
Tony Pulis' side currently sit three points above the trapdoor, but they have played two games more than third-bottom Wigan Athletic.