Steaua Bucuresti and Stuttgart have progressed to the Europa League round of 32 from Group E.
Copenhagen finished the group level on eight points with their German rivals, but lost out on an inferior head-to-head record.
Dnipro have won Group F with 15 points from six matches with a comprehensive 4-0 win against AIK Solna at home.
In other early evening kickoffs in the Europa League, Hapoel Tel-Aviv defeated Academica 2-0 at home in Group B, Marseille lost 3-0 at AEL Limassol in Group C and Maritimo won 2-1 against Club Brugge in Group D.
Europa League results: Young Boys 3-1 Anzhi Makhachkala; Hapoel Tel-Aviv 2-0 Academica; AEL Limassol 3-0 Marseille; Maritimo 2-1 Club Brugge; Copenhagen 1-1 Steaua Bucuresti; Stuttgart 0-1 Molde; Dnipro 3-0 AIK Solna; Napoli 1-3 PSV Eindhoven