Hi,
Yes, there is a route Berlin Hbf to Vienna (Wien Westbahnhof) that goes through the Czech Republic and since your 3 country Pass does not cover transit in the CR, just buy a ticket at any DB ticket counter for that portion of the ride.
BUT, I don't recommend that, that's extra cost on top of your Pass. No need to pay extra to go through the CR. With your Pass you can do the entire route Berlin-Vienna w/o paying extra.
What I do in your case going from Berlin to Vienna day or night is to transfer in Munich, ie, go Berlin-Munich Hbf direct on the ICE, then transfer to the Rail Jet train to Wien West.. This way all costs are covered by your Pass since you're going through Germany and Austria, both of which listed on your Pass, unless you want to get a reservation for either or both legs, neither of which is mandatory.
If your Select Pass is 1st class, you may sit in 1st or 2nd class in the ICE or the RJ. If not, just hop on the ICE, look for seats w/o any electronic writing above the seat eg. Berlin-Leipzig or if the electronic wording is "bahn.de," that's ok too...the seat is unoccupied. In 2nd class the reservation is ca. 4-5 Euro.