What should I use to seal the ball rod on a pop-up sink drain plug?
Every lavatory faucet manufacturer also supplies the pop-up assembly; they are ALL different. There are also many replacement units from manufacturers all over the globe; again, all different. 

Unless you know the manufacturer and source an identical replacement, you will need to find a tapered washer of some sort that fits the nut and ball. It might be shaped something like this:



You will likely need to change out the whole pop-up assembly or do what I have done: throw away the stopper, rod, linkage and nut. Plug the hole where the rod went in with plumber's epoxy. use a rubber stopper on a chain.