The 18-year-old striker netted twice as captain Nemanja Vidic — and possibly club legend Ryan Giggs as well — departed Old Trafford victorious.
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 a 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 stadium.
The Welshman had time to supply Robin van Persie with the ammunition for the hosts' third goal, too, with the Dutchman's initial effort blocked by Curtis Davies before he buried the rebound. Giggs nearly even scored a fantastic late free kick, though it was well saved by Eldin Jakupovic.
Victory means that United could still overcome Tottenham and steal the 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 teammate, 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 lackluster first-half display continued into the second period as United went close to doubling its lead. The effervescent Januzaj found space 25 yards from goal before firing a low shot toward 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 to create the chance and Fellaini seeing his 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, with the Welshman making an immediate impact and producing some dazzling wing play that turned back time to the days when he so frequently terrorized 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, with the Dutch striker receiving a pass from Giggs before firing past Jakupovic at the second attempt to wrap up a comfortable victory.