With qualification as group winners already secured, interim boss Ralf Rangnick took game as an opportunity to see more of his players in action.
The German made 11 changes from the United XI that started his first match, against Crystal Palace at home in the Premier League win last Sunday.
Rangnick's Reds took the lead with an athletic hit by Mason Greenwood after just eight minutes, but Young Boys equalised late in the first half through Fabian Rieder.
A competitive second half then played out in wet conditions at the Theatre of Dreams, where senior debuts were handed to Tom Heaton, Charlie Savage and Zidane Iqbal, as well as Champions League bows for Amad, Teden Mengi and Shola Shoretire.