The Cameroon forward put the hosts ahead with his opener but they failed to protect their lead in the second 45 minutes
The 27-year-old striker stepped forward to put the hosts ahead from the spot in the 14th minute after Fabian Rieder was fouled in the penalty area.
The strike was Nsame’s third goal in the European tournament this season after he fired them into the group stage with his brace in their 3-0 win over Albanian club Tirana on October 1.
The Cameroon international’s opener was not enough for the Swiss champions to secure maximum points as Roma staged a dramatic comeback after the interval to overturn the result.
Bruno Peres grabbed the equaliser in the 69th minute and Marash Kumbulla scored the match-winning goal for the Serie A club four minutes later.
Nsame was in action for Young Boys alongside his compatriot Moumi Ngamaleu, and they were both replaced in the 79th minute and 65th minute respectively. Meanwhile, DR Congo’s Meschack Elia was introduced five minutes after the hour-mark and Guinea’s Mohamed Camara watched on as an unused substitute.
Nsame who scored 32 goals in 32 league matches last season, will hope to build on Thursday’s strike when Young Boys welcome Luzern to Stadion Wankdorf for their next Super League fixture on Sunday.
Thursday’s defeat moved Young Boys to third in their Europa League Group A table, behind CFR Cluj and Roma. In the Swiss top-flight standings, they are third with eight points after four games.