Farhadi boycotted the ceremony, with two Iranian-Americans representing him.
"Dividing the world into the US and 'our enemies' categories creates fear," his acceptance statement read.
US courts have blocked the travel ban but the Trump administration is preparing a new executive order.
The original ban temporarily prohibited the entry of immigrants from seven Muslim-majority countries.
One of those chosen by Farhadi to represent him, Iranian-born US engineer and astronaut Anousheh Ansari, read out his acceptance statement.