United are often accused of starting the game slowly, but in the first 45 minutes they pressed with swift incisive passing, pushing Young Boys back onto the defensive.
The fact the scoreline was blank at the interval was more due to poor finishing from the home side than sound defence from the visitors.
Marcus Rashford was the chief culprit with three good chances falling to the England international, the first after only 5 minutes but in trying to chip the keeper David Von Ballmoos he also cleared the cross bar. Further efforts went wide and one was saved.
Brazilian Fred, on a rare outing for the first team, hit a long range shot narrowly over as the Swiss outfit struggled to break out and create any meaningful chances.
Young Boys may be running away with their league but this was a step up in class and was showing and whilst the score remained scoreless they were still in with a chance of nicking a win which would see them with a chalice for qualifying for the Europa League competition.
And just before the break their chance came from a quick break but from close range Djibril Sow attempted an ambitious flick when a simple shot would would have been productive. A warning for Utd.
Young Boys it was who had the first chance in the second half when Kevin Mbabane fired into the side netting only for Rashford to drag his shot wide from a good position at the other end.
Young Boys were looking more confident whist Utd seemed to have lost their edge from earlier much to the delight of the vocal travelling Swiss supporters.
Again Rashford went close as Paul Pogba and Romelu Lukaku came off the substitutes bench. A quick break almost set up Anthony Martial but then David de Gea made a remarkable save low down on the line from Michel Aebischer to prevent the Swiss from taking the lead.
The hosts began to get frustrated and their play became ragged with Young Boys looking the more dangerous.
The final whistle was greeted with relief from the Old Trafford faithful as Marouane Fellaini reacted quickest to a knockdown to fire home in injury time and break Swiss hearts.
Full Time Group H
Man Utd: (Fellaini 90)
Young Boys: 0