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1.
When a guy is having sex in the doggy-style position and spits in her anus and slowly and silently slides his fingers, usually his thumb or middle finger, into his woman's anus for better stimulus and for his own self-enjoyment of the moment, gently stroking it in and out, with the hopes that she doesn't mind or won't say anything! That's a silent ninja!

On the bad note: It could also be reversed too. A wicked girl can give her boyfriend a silent ninja too! And he might end up liking it!!!!
Last night I gave my girl friend a silent ninja and she didn't mind. I guess she likes it in the ass after all?
by Attila the Milf Hunter July 29, 2010
 
2.
A fart that goes by silently, and everyone but you can smell it.
jon let off a silent ninja.
by El Skeeto April 05, 2007