In most cases of usage of the discounted tickets (including SparSchiene from Austria to Germany) passengers can not interrupt their journey (unless ticket is issued for multiple leg journey, in such case waiting time is minimal and all the legs(=specific trains) must be listed on the ticket)
Unfortunately, but in your case you will have to buy two separate tickets - full fare for Vienna-Durnstein (15.7 euro) and discounted Durnstein-Munich (from 29 euro, purchase in advance here -
https://ticket.oebb.at/bin/frame_ticket.pl?ticket=jticket.pl&LANG=EN).
But in case you plan to travel with somebody or/and plan to make a trip Vienna-Durnstein-Munich in one day, then you might consider better option - Einfach-Raus-Ticket (special group pass, allows up to 5 passengers to travel the whole day long on any regional trains* in Austria, more info -
http://www.oebb.at/pv/en/Travelling_cheaper/Groups/Einfach-Raus-Ticket/index.jsp). It cost 28 euro, thus it makes sense instead of 2 full fare tickets Vienna-Durnstein. If the trip is done in one day, then you can easily use same Einfach-Raus-Ticket till Salzburg. There you buy Bavaria group ticket and continue to Munich.
Purchase of Einfach-Raus-Ticket and Bavaria ticket doesn't require any advance booking, so such combination of group tickets can be used any time. While Sparschiene tickets have limited availability and in order to ensure purchase of 29 euro ticket you will need to book quite long time before the journey.
* Vienna-Krems-Durnstein route is served only by regional trains, so Einfach-Raus-Ticket is valid for such trips.