The 18-year-old striker, given his first start as well as Tom Lawrence, netted in either half, while Matty Fryatt's fine long-ranger was made irrelevant by Robin van Persie
The youngster, along with Welsh winger Tom Lawrence, was fielded by Ryan Giggs for his maiden first-team game and made it a memorable one half an hour in when he fired home with a left-footed volley.
The Red Devils extended their lead through Wilson just after the 60-minute mark when he tapped in on the rebound, though the Tigers got a consolation in fine style with Matty Fryatt's long-range stunner only two minutes later.
Old Trafford also had a chance to say goodbye to captain Nemanja Vidic, who came on for one last home game before joining Inter in the summer, while 40-year-old Giggs brought himself on in the second half for what is expected to be his final playing appearance at the ground.
|VIEW FROM OLD TRAFFORD
|By Tom Maston
On a night more about sentiment than Premier League points, Manchester United's young guns showed that there may still be some life after the likes of Ryan Giggs and Nemanja Vidic have left the scene.
Teenage striker James Wilson displayed a good eye for goal while Chris Smalling and Adnan Januzaj both put in outstanding performances.
Few will remember this match for the action but it was a fitting send-off for those set to depart this summer.
Victory means that United could still overhaul Tottenham and steal sixth spot on the final day of the season, while defeat for Hull extends Steve Bruce's winless run against his old club as a manager to 20 games.
Giggs made eight alterations to the side beaten by Sunderland on Saturday, including blooding the two youngsters, while his former United team-mate, Bruce, also made changes with the upcoming FA Cup final in mind.
Bruce's men were lucky to avoid conceding a penalty when Adnan Januzaj was tackled by Maynor Figueroa and the Honduran defender was in the thick of the action again when Lawrence's 16th-minute shot struck him on its way over the crossbar.
The deadlock was finally broken after 30 minutes without a shot on target by Wilson following a Januzaj free kick. The young striker latched onto a knockdown from Fellaini, the Belgian's first assist of the season, and instinctively volleyed the ball into the bottom corner.
Hull's lacklustre first-half display continued into the second period as United went close to doubling their lead. The effervescent Januzaj found space 25 yards from goal before firing a low shot towards goal that Jakupovic had no problems pushing away for a corner.
United did get a second goal after 61 minutes and again it was Wilson who was on hand to score. After more excellent work from Januzaj and Fellaini seeing an effort saved, the teenager pounced on the loose ball to double his tally.
Substitute Fryatt found the bottom corner two minutes later with a superb curling effort from 25 yards to give Hull hope.
Wilson was then replaced by Van Persie and Giggs also came off the bench, the Welshman making an immediate impact and producing some dazzling wing play that turned back time to the days when he so frequently terrorised defences.
David Meyler had a late chance to snatch a point for the visitors but David de Gea was equal to the task.
And Van Persie punished Meyler's miss late on, the Dutch striker receiving a pass from Giggs before firing past Jakupovic at the second attempt to wrap up a comfortable victory.