A Santi Mina double saw Valencia achieve their first win in Europe this season and apply more pressure on Manchester United who play later against Juventus.
The home side were on the attack from the first whistle and could have gone ahead after four minutes but Rodrigo had been adjudged offside after putting the ball in the net.
The Spanish forward’s first goal of the night came after tapping in a rebound from close range. Initial good work saw key winger, Carlos Soler rattle the post in the 14th minute when he got on the end of a pass but smashed it straight on to the left post.
Minutes before half time, the Swiss champions levelled after superb work from Christian Fassnacht so him square it to forward Roger Assale, who beat goalkeeper Neto with a shot into the bottom left hand corner.
On the stroke of half time, the 22-year old forward edged Valencia back in front after finding some space inside to box to meet a cross and finish into the bottom corner with a low shot.
Young Boys could have levelled a minute later when left winger, Ngoumo Ngamaleu blazed over the crossbar after darting into the box unmarked.
The Swiss champions were out of the blocks quickly and key forward Guillaume Hoarau squandered a vital opportunity when he put his free header wide of the post from point blank range.
Hoarau, who has five goals in his last six appearance in all competitions was made to rue that glorious chance when Spanish midfielder Carlos Soler danced his way through the Young Boys defence, beating David von Ballmoos with a low strike into the bottom left corner.
Tempers started to flare fifteen minutes from time and midfielder Sekou Sanogo Junior saw straight red after clattering his opponent with an awful tackle.
In injury time, Los Che could have added to their goal difference and put more significant pressure on Manchester United, but makeshift right-back Daniel Wass drilled a strike straight at the keeper from inside the box.
Marcelino’s men jump into second for the time being on five points and will be hoping to replicate their game plan against Getafe on the weekend.