For a jurisdictional boundary the commonly accepted point is the Karman Line 100 kilometers above sea level. The idea is that manmade objects above that line are spacecraft and certain agreements apply to them, and below that are aircraft and different agreements (like territorial and airspace sovereignty) apply to them.

From a more sciency answer, the atmosphere thins out and there is a measure where they say it's not really atmosphere anymore. However, it is not uniform, in that kind of like waves on the sea, the "surface" of the atmosphere isn't flat but fluctuates.