Arsenic Prevention and Protection from Lead Exposure in Juice Act of 2012 or the APPLE Juice Act of 2012 - Directs the Commissioner of Food and Drugs (FDA) to promulgate final regulations establishing tolerances under the Federal Food, Drug, and Cosmetic Act (FFDCA) to limit the quantity of total arsenic and lead in beverages containing fruit juice. Requires the limitations on total arsenic and lead in such beverages to be no less stringent than the allowable level for total arsenic and lead in bottled water under the FFDCA. Provides that if there are no such tolerances in effect within two years, a beverage containing fruit juice shall be deemed to be adulterated if the quantity of total arsenic or lead in the beverage exceeds the limits of the allowable level for total arsenic or lead, respectively, in bottled water.