The words "divide" and "distinguish" both work perfectly well. Merriam-Webster lists this sense for each of these words.
divide (v.) 1b. to separate into classes, categories, or divisions - divide history into epochs
distinguish (v.) 2b. to separate into kinds, classes, or categories - distinguish words by their part of speech
Which is better? That's subjective. Personally I prefer "distinguish", because I feel like the primary meaning of "distinguish" is closer to your intended meaning.
I would say that the distinctness of these classes is pretty much implied, so it's unnecessary to add the adjective "distinct" - especially if you use the verb distinguish, which strongly implies a distinction between things.
The preposition you place after these words ("in" or "into") is a little tricky. You can divide a cake into many slices, but you also can divide a cake in half. In your example, you would follow the verb "divide" with the preposition "into": e.g. the properties of matter are divided into three classes. But if you use "distinguish", then you would follow the verb with the preposition "in": e.g. the properties of matter are distinguished in three classes.