Tokens appear to be Gilead's version of a ration stamp. Tokens are used as part of the general wartime rationing system, or possibly because Gileadean women are not permitted to handle money directly, necessitating the use of the tokens.
They are mentioned rather early on in the novel, on page 24 Offred is in Milk and Honey and sees oranges and says in her mental dialogue; "I look at the oranges, longing for one. But I haven't brought any tokens for oranges."