But do we know for sure, who was the first villain to use kryptonite against Superman?
Where did they obtain it and how did they know / discover it was his one weakness?
I'm hoping all these details are covered in the same story.
The first use (in any media) was in the radio play "The Scarlet Widow" from 1943. The eponymous villainess steals kryptonite from the Metropolis Museum and uses it to build a cage for Superman, incapacitating him for several episodes.
Interestingly, the plot device was apparently intended to give the Superman voice actor (Bud Collyer) a few days holiday as his character was restricted to pre-recorded grunts and screams.
The first use in any comic serial was from Superman #61 ("Superman Returns to Krypton"). Superman fights a self-styled Swami whose kryptonite turban-stone causes Superman to become weakened. This edition is also famous for being the first time that we see the planet Krypton in a non-exploding state.