The hosts headed into the game with two wins from their first two games but looked to be on the way to losing their 100 per cent record when first-half goals from Josef Martinez and Marco Schneuwly saw them trail 2-0 at the break.
But half-time substitute Yuya Kubo had the desired effect, his brace getting his team back on level terms within 20 minutes of the restart before Moreno Costanzo sealed the comeback with the winner 13 minutes from time.
The win moved Young Boys two points clear of Grasshoppers and Basle at the summit.
Lucerne also enjoyed a 3-2 home win today, beating FC Zurich and climbing to fourth spot as a result.
Oliver Bozanic and Dario Lezcano put the hosts two goals up at the interval and, although Mario Gavranovic pulled one back in the 59th minute, Bozanic's second of the game swiftly re-established the two-goal cushion before substitute Pedro Henrique's last-gasp consolation.
In Sunday's other game, Philippe Montandon's ninth-minute strike was enough to earn St Gallen their first points of the campaign with a 1-0 triumph at FC Sion.
Belgian Jupiler League
Lokeren provided the shock of the opening weekend in the Jupiler Pro League with a 3-2 win away to reigning champions Anderlecht.
Hans Vanaken scored twice and new signing Jordan Remacle sealed victory for Lokeren, who impressed last season in reaching the Championship play-off before fading to finish sixth.
Massimo Bruno had drawn Anderlecht level at 1-1 but Guillaume Gillet's 76th-minute penalty was mere consolation.
Standard Liege claimed a routine 2-0 win away to KV Mechelen to slot in alongside Club Brugge behind week one leaders Genk.
Geoffrey Mujangi Bia set them on their way in the 57th minute and Michy Batshuayi sealed victory six minutes from time.
Russian Premier League
CSKA Moscow recorded their second win in the opening three Premier League games with a 2-1 success away to cross-city rivals Lokomotiv.
Ahmed Musa scored the winning goal eight minutes from time, eight minutes after Lokomotiv's Dmitri Tarasov had cancelled out Keisuke Honda's first-half opener.
Anzhi Makhachkala, under new coach Rene Meulensteen for the first time, were held to a 1-1 draw away to Krylya Sovetov.
Samuel Eto'o gave Anzhi the lead shortly before the hour mark but substitute Roman Vorobyev equalised with a deflected effort eight minutes from time.
The day's other game was also drawn as Terek Grozny and Rubin Kazan failed to muster a goal.
Helsingborg moved five points clear at the summit of the Swedish Allsvenska after coming from behind to secure a 4-2 win over IFK Gothenburg.
Gothenburg led 2-0 thanks to goals from Robin Soder (22) and Tobias Hysen (26), but Loret Sadiku pulled one back three minutes before the interval and David Accam levelled on the stroke of half-time.
The momentum stayed with Helsingborg after the restart with Mattias Lindstrom making it three in the 52nd minute. Accam's second sealed the win in the final minute.
Second-placed Malmo fell off the pace of the leaders after a 2-0 loss at Gefle, who took the lead through Simon Lundevall (13) before Johan Oremo (48) made it two.
FC Copenhagen suffered a second successive defeat to begin their Superliga campaign as Midtjylland won 1-0 on Sunday.
Petter Andersson's goal after eight minutes was enough to upset Copenhagen, champions last season and for eight of the last 11 years, and take Midtjylland top of the fledgling table, having won both of their games without conceding a goal.
Sonderjyske were also 1-0 winners, Nicolai Madsen scoring just after the hour mark to defeat Brondby.
Odense came from behind to draw 1-1 at Randers in the day's other game. Bashkim Kadrii struck 12 minutes from time to cancel out Ronnie Schwartz's opener.