The section of rail between Venice and Vienna (which I imagine would be part of the route) is rated as one of the best 10 train trips in the world. Having done it I would have to say you'd be crazy to fly over the countryside the track passes through - do it in daylight.
There's a good Austrian sleeper train from Venice Santa Lucia (on the very banks of the Grand Canal in central Venice) to Vienna Westbahnhof, Venice depart 20:57, Vienna arrive 08:08.
Fares from €39 with a couchette (simple flat bunk with rug and pillow) or €69 with a bed in a cosy 2-bed sleeper with washbasin, light breakfast included.
Book this sleeper train at www.italiarail.com (easier to use than www.trenitalia.com for this particular train) with ticket collection from the easy-to-use self-service ticket machines at any main Italian station.
Or see something of Vienna and take a later one!Edited: 2:37 am, March 19, 2013
Man in Seat 61 - I love your work and your website, but to suggest that someone take an overnight train from Venice to Vienna sells the journey short imo. I know that OP mentioned overnighting, but it's one of those trips that just HAS to be done in daylight.
Problem is, Verona-Innsbruck is a long way round, and since Trenitalia pulled out of the two daytime trains, there's nothing but a bus.
12 hours train. That's a lot of time in a train...This being said, it seems you can do it by night train at the end of May (I checked May 24th and 25th): two successive night trains, change in Salzburg at 4am. Alternatively you could fly Air Berlin (One way USD 200 on the same day, change in Berlin).