Digital copies of games can now be purchased and downloaded from Nintendo’s official website, Nintendo.com. Players who wish to pre-order or purchase full games can enter their Nintendo Network ID and have the game sent to their system automatically, or can choose to receive their purchase as a downloadable code to be entered later.
At present the range of games available on the site is quite limited, but is expected to expand with time. It currently includes major titles such as Super Smash Bros. for 3DS and Fantasy Life. The website also includes an option for players to see a range of third-party retailers selling physical copies of the game.
Source: My Nintendo News