Despite their emphatic win, United ended the season in second place with Chelsea claiming the Premier League title with a victory against Wigan.
Wayne Rooney inability to finish the game was the most noteworthy development of a flat game, though, and one that will concern Capello as he prepares to name his 30-man squad for South Africa.
The England manager will now wait for news on Rooney, who limped off clutching his groin on 76 minutes before being replaced by Ji-Sung Park.
Regardless of United's result against Stoke, their destiny was always firmly in Chelsea's hands and, with Nicolas Anelka scoring an early goal to put the London club ahead against Wigan at Stamford Bridge, the faint hope of an Old Trafford title party was extinguished before United even hit their stride against Tony Pulis' team.
But United still had to play for the victory that might just have accompanied a remarkable Wigan fight-back in west London.
So it was no surprise that the outgoing champions pummelled Asmir Begovic in the Stoke goal as they attempted to find an early opener.
Dimitar Berbatov went close in the fifth minute when his angled shot was blocked by full-back Andy Wilkinson and the Bulgarian forward was unlucky again six minutes later with a header from close range that flew narrowly over the crossbar.
Berbatov has had little luck in recent weeks, with his form in front of goal evaporating in the run-in. Not since the victory at Bolton at the end of March has the former Spurs forward added to his tally of 12 goals this term.
And his wayward finishing returned again on 23 minutes when he rattled the Stoke bar from Nani's pinpoint cross.
Fletcher rewarded United for their dominance on 30 minutes, though, when he reacted to a loose ball in the penalty area following Ryan Giggs's corner by scoring from two yards to make it 1-0.
With Stoke's resistance broken, United doubled their lead on 38 minutes when Giggs scored from close range after Nani had dummied Berbatov's cross for the Welshman to beat Begovic.
Celebrations were muted, though, with news of Chelsea's second goal against Wigan quickly filtering through to Old Trafford.
The title race was over and the United supporters knew the game was up.
Despite the flat atmosphere, though, the anticipated anti-Glazer protests failed to materialise inside the stadium, apart from sporadic chants against the club's American owners.
On the pitch, it continued to be business as usual for United, however, with an own goal - the 12th in United's account this season - making it 3-0 on 54 minutes.
Rooney's cross was heading for Nani before former United defender Danny Higginbotham sliced the ball into his own net from three yards.
Game over for Stoke, but United rounded off the victory on 84 minutes when Park scored with a diving header to end the season with a comprehensive victory, if not the title.
Source: Telegraph
Source: Telegraph