Generally, DB does not sell tickets online for train travel starting and ending outside of Germany. However, the short distance of track from the border into Salzburg is run by DB and the Salzburg Hbf is considered a border station. Therefore, tickets for a trip starting in Salzburg, but going immediately into Germany and from there to the Czech border to Prague will be offered by DB.
Such is the case with the all regional connection leaving Salzburg at 9:11 and going through Landshut, Regensburg, and Schwandorf. You can find this connection on the DB site and it gives a fare of €55,70.
You could also do this trip for less by buying "Anschluß tickets" from Furth im Wald to Prague for €18,70 per person and using a €27 Bayern-Ticket from Salzburg to Furth. That uses the same trains as the €56 per person ticket.