If I heard this right, it refers to the action of being sexed half-willing, whether out of obligation or whatever motivation (this isn't referring to rape, mind you). It comes from a movie called Dog Park, and I'd like to see the term used more.
"How'd it go last night? Well, she ninjafucked me."
When you ( a male) is having sex with two other people ( male or female) and you fuck them in the butts back to back. Hence, you see an ASS, you see an ASS, and you went IN, or assassin ( which is a word used to describe a ninja).
Joe Schmoe: Hey bro, I just had a consecutive buttsex with these two smoking hot chicks last night
Douchebag Dan: Duuuuuude! You just had a Ninja Fuck!!!
Joe: Totally gnarly dude!!