Gabon lost 3-0 to Morocco over the international break and missed out on a place at the 2018 World Cup.
Bosz says the BVB star is disappointed at his country's failure to qualify although he doesn't think the striker will allow it to impact on his club form.
Christian Pulisic also failed to reach the tournament in Russia with the USA and Bosz hopes the 19-year-old forward's confidence won't be affected.
"Yes, [Aubameyang is hurting] and you can imagine the same with Pulisic," he told reporters ahead of Saturday's visit of RB Leipzig. "It is always difficult. On the other hand, we must go on. We've talked about it."