The 18-year-old striker was trusted by interim manager Ryan Giggs to lead the line in United's final home game of the season on Tuesday and he rewarded that faith by finding the net in either half, much to the delight of the Old Trafford faithful.
Wilson's first came in the 31st minute after Marouane Fellaini's assist and the teenager added a second just after the hour from close range.
Substitute Matty Fryatt pulled a goal back for Hull two minutes after Wilson's second of the evening before Robin van Persie restored United's two-goal cushion with four minutes remaining with his first goal since March, a drilled effort from the edge of the penalty.
Victory means United - who lost defender Phil Jones to a shoulder injury midway through the first half - can overhaul Tottenham and steal sixth spot on the final weekend 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 as youngsters Wilson and Tom Lawrence were handed their first-team bows.
Hull counterpart and Giggs' former United team-mate Bruce also made changes, no doubt with the upcoming FA Cup final in mind, and the visitors struggled to make any impact in the opening exchanges.
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, his 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 Eldin 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 saw an effort saved, Wilson 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 to make what could be his final appearance as a player at Old Trafford.
The Welsh winger made an immediate impact and produced some dazzling wing play that turned back time to bygone days when the 40-year-old 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.
