It depends. If the Ninja was Michael Dudikoff's character Joe from American Ninja, the Ninja would win.
I can just imagine the Jedi going like Steve James' character Cpl Jackson something like, "There are some people who think they are Bad Asses. And then there are those of us who ARE." :rofl: Then Joe went on to kick Jackson's ass. :rofl2:
Then again, if the Ninja is just your regular run of the mill, off the rack Ninja of the type that Michael Dudikoff's Joe and Chuck Norris' characters have dispensed of easily, then the Ninja is toast against the Jedi.
Who knows? Maybe the Jedi will be in awe of the Ninja's cooler uniform and while distracted, get his ass kicked.