Main route is Brenner. That means Munich - Garmisch - Zirl - Innsbruck - Brenner. From Zirl to Brenner Motorway its 11km on the A12. Brenner Motorway is not included in the vignette system and costs extra toll.
Another North-South transit route is Kufstein - Felbertauern. From border to Kufstein-Süd its 6km. Again Felbertauern costs extra toll.
Pfändertunnel is about 10km, after the tunnel you can switch to the Swiss motorway, which you need anyway if you are going South to Italy.
A fourth route would be Garmisch - Fernpass - Landeck - Reschen, which is not so popular. Here its 12km motorway and the tunnel around Landeck which is not a motorway, but is included in the vignette system.