PC Chris Dwyer, 51, paid just 10p for the chocolate-covered treats but claimed he had paid the correct amount of £1 when challenged by a colleague.
He then "changed and embellished" his story when quizzed about it and said he could not remember what coins he had placed in the charity tin at Halifax police station.
West Yorkshire Police said a female officer had emptied the charity shop cash tin at around 10pm on January 21 and left a £1 float in change.
Half an hour later, PC Dwyer allegedly took two packets of Jaffa Cakes, priced at 50p each and did not leave any money.
A spokesman said: "The cash tin was checked and it was found to contain the same denominations of coins in the cash tin but with an extra 2 x 5p coins."
PC Dwyer, who spent nearly 25 years in the navy before joining West Yorkshire police in 2017, said any underpayment was a “genuine mistake”.
But he was given an instant dismissal on Thursday (October 14) after a four-day misconduct hearing found him guilty of gross misconduct.
Detective Superintendent Mark Long, of West Yorkshire Police’s Professional Standards Directorate, said: “This officer’s actions do not fit with the values of the organisation and he has been dishonest when challenged.
"It is accepted that the items involved were of a very low value but honesty and integrity is a fundamental quality of being a police employee.
“An independent legally qualified chair has found that his breach of the Standards of Professional Behaviour constituted gross misconduct and he has been dismissed from the Force.”