Actually, you could save yourselves a few euros by booking on the OeBB site from Scharnitz (to Venice etc) rather than from Innsbruck. It's the first station in Austria on the Garmisch - Innsbruck line, and the advance fares are the same as from Innsbruck.
Then you only need to buy a Garmisch - Scharnitz ticket (currently €9.90 per person). This doesn't affect your journey at all - you don't have to get off the train at Scharnitz.