I don't think that keeping them stuffed with paper towels / newspaper for the entirety of the drying process is the way to go. The paper absorbs a lot of water, yes, but eventually an equilibrium is reached and it's just damp everywhere. I've found that one or two cycles of, say, two hours with the stuffing is good, but you should let the shoes air dry - without the stuffing - after that.

I had just the OP's situation yesterday on both legs of my commute. I did as I said above, and they were dry both by the time I went home last night and by the time I left the house this morning.