When you discharge a lithium-ion battery all the way you can run into serious problems. If the battery is relatively new it may be under warranty and an exchange would be your best bet.
The battery contains electronic circuitry designed to prevent a total discharge. If that circuitry fails the battery is ruined. If the internal voltage of the battery falls below a critical level this circuitry will NOT allow the battery to charge. Your charger's refusal to charge the battery indicates a problem with this circuitry.
If your other options don't work, and you can't exchange the battery for a new one, you can try putting the battery in your fridge (not the freezer) for an hour or so and see if that will help jump start it. Cool for an hour and try charging.
In my experience, once this happens to a battery it's well on it's way to being dead forever, even if you can recharge it once or twice.