So Venice or Vienna?
If we are talking about Vienna-Prague overnight, then we deal with direct carriages, that only get reattached from one train to another in Breclav, you don't need to get off train.
In terms of tariffs
OEBB unfortunately doesn't sell discounted tickets for those overnight carriages (ups... just rechecked it differently and found out that OEBB actually sells those as well, same 29 euro as to Dresden, sorry), so in addition you have a number of solutions: 1) to buy regular fare ticket (app. 60 euro); 2) buy discounted ticket from Vienna to Dresden on OEBB website (from 29 euro seats, 39 euro couchette), but get off train in Prague; 3) buy regular international Vienna-Breclav/Brno ticket + Czech domestic Breclav/Brno-Prague (this one here -
https://www.cd.cz/eshop/search.aspx), both for the same train; 4) go Vienna-Bratislava (train from 14 euro) and catch there overnight to Prague (around 23 euro for the ticket + 9 euro for couchette or app. 11.3 euro for 3 bed sleeper).
Fares for daytime trains Vienna-Prague start from 29 euro (seats), if purchased some time in advance.