You obtain Elemental Tokens as a reward from PVP Arenas.
Once you have completed a Elemental Arena you are rewarded with Elemental Tokens to upgrade your habitat of that element.
Please note: You only get the Elemental Tokens reward ONCE (the first time you are promoted to a new Arena!). If you're demoted and promoted again, you don't get the reward a second time.
Example: Once you have completed all of the Terra Arenas (Terra I and Terra II), you are rewarded with Elemental Tokens to upgrade some of your Terra habitats!
Note: in the future you will have other ways to obtain Elemental Tokens in the game!