There are just a couple of high end cars with automatic in Sixt Austria like the BMW X5 SUV (XFAR). On the website you can select "Automatic preference" in the extras section but it is not guaranteed.

I would call the station where you plan to rent the car and ask them which cars they have with automatic and how to get a reservation for exactly that car.

Alternatively look at Hertz, Avis and Europcar.

At Hertz you can select a automatic car directly at the booking at lower prices in group IDAR, e.g. in Vienna the Mercedes A-class, at Europcar you can get a confirmed automatic in the Mercedes C-Class group and at Avis in H (Mercedes C-Class), I (Mercedes E-Class), and J (Mercedes GLK-Class).

Anyway, automatics in most of Europe come at a premium price with very limited availability.