As every item is capable of being thrown, the lists are quite extensive so use this table to navigate to see what item corresponds to the power
So, you would fling the Master Ball, deal damage, and then lose it, unless it is a Wi-Fi battle, in which case, you will get it back after the battle.
Source - Serebii's Fling move page
On Serebii, it says it has a Fling Damage of 30, don't know what Fling Damage means but I'm sure it means that it can be Flung.
Source - Serebii's Master Ball ball page