Guillaume Hoarau followed up a first-half spot kick with a splendid long-range drive to finish off a flowing counter attack and condemn the Bianconeri to defeat in Massimiliano Allegri's 50th match in charge in the competition.
Substitute Paulo Dybala pulled one back with a thumping effort 10 minutes from time, and then had a stoppage time strike ruled out, with Cristiano Ronaldo adjudged to have been in an active offside position.
However, the Old Lady's first away defeat of the season had no further implications as Manchester United's 2-1 reversal in Valencia ensured they finished above Jose Mourinho's men.
Valencia were third in the pool with Young Boys already stuck in bottom place ahead of this famous victory.
An off day for the Old Lady with no major implications.
Juventus equalled the best-ever start to a campaign in the top five European leagues in the three-point era with a 1-0 victory over Inter Milan on Friday, so this defeat will surprise many.
Was it complacency or perhaps trouble with the plastic pitch? Ronaldo and Co were already through and United's loss means the Italians will look to brush it off and put it down to a bad day at the office, though many will feel Paulo Dybala should have been introduced much earlier.
Regardless of this result and the inevitable Italian media post-mortems, no-one will fancy drawing Allegri's men in the knockout stage.
MAN OF THE MATCH
Guillaume Hoarau (Young Boys). The forward held his nerve from the spot to net his 100th goal for the club before adding another match-winning strike to cap a lively display leading the line.
YOUNG BOYS: Wölfli 8, Mbabu 8, Camara 8, Benito 7, García 6, Lauper 7, Ngamaleu 8, Aebischer 7, Sow 8, Hoarau 9, Fassnacht 7. Subs: Bertone n/a, Schick n/a, Wuthrich n/a.
JUVENTUS: Szczesny 6, De Sciglio 6, Bonucci 6, Rugani 6, Cuadrado 5, Pjanic 6, Bentancur 6, Costa 7, Bernarderschi 6, Ronaldo 6, Mandzukic 6. Subs: Sandro 5, Can 5, Dybala 7.
SHARE THIS STORY USING ANY OF THE BUTTON BELOW ⬇ PLACE YOUR TEXT ADVERT BELOW ⬇⬇⬇