Is it permissible for an accountant to take a portion of the money he saved for the company when purchasing supplies for less than the usual price, provided that the total price remains lower than what they were accustomed to dealing with?

It is not permissible to take anything from the company's funds without its knowledge and consent. If this occurs, it constitutes treachery and unlawful consumption of wealth. Your ability to purchase at a lower price than what they buy does not justify taking money without right, for the agent is a trustee who acts in the best interest of the principal.