I'm not sure about this. I did it and both cars stayed in the same garage (checked a short time after). But will this be permanent or will one car be removed if I stay to long away or something similar?
You can indeed store multiple in one garage, if you squeeze them in. So long as they fit, they will save.
Edit: To edit my post to best answer the OP, they will save and the cars will stay there until you go back to the garage and remove one yourself.
Edit 2: More information on GTA V garages.
Each character has a purchasable 4 car garage, in these you can only store 4 cars.
You can store 2 cars in Michael's safehouse garage, 2 at Franklin's Safehouse garage, and 1 at each of Trevor's safehouse garages.
This leaves you with a grand total of 18 cars you can store in Story Mode. 50 for gta online, however.
Edit 3: More information on GTA Online Garages
As of the 'executive and criminals dlc' in gta online you can total buildings/apartments with garages that hold between 2-10 cars. You can buy 5 parking garages/high-end apartments (which have 10 car garages) for a total of 30 saved cars.
Thanks VanBuzzKill for the GTA Online information