I think it's a loan word. The root "alien" exists in words like *alienado* (alienated) or *alienação* (alienation), but as a single word alien/aliens I think comes from English.
My memory failed for a bit, as another commenter said, the actual word for alien in Portuguese is *alienígena*, but nowadays many shorten it to alien (likely due to English influence)
A bit of a correction, alien has its roots in Latin, alius (other) -> alienus (belonging to other), which spread over the places the Romans conquered. Since it's Latin, it's also the why most legal documents love using "alienate" when it comes to transferring ownership of stuff
No idea when alien started to be used to refer to extraterrestrials.
I literally said my explanation didn't make sense. I'm not sure what more you want from me. I have yet to get my time machine in functional order. I think I misread the instructions from IKEA.