That means Travelcards, monthly Oyster cards and daily caps will not be included.
Liberal Democrat London Assembly Member Caroline Pidgeon told Mr Khan: "I think you have broken your fares promise today."
During a session of the London Assembly, the Mayor said the Department for Transport (DfT) sets fares for train services, adding: "I can't make the Government do what I'm doing."
He later posted a message on social media claiming that his election pledge had been "delivered in full".
His manifesto stated that he would "freeze TfL transport fares for four years" and "Londoners won't pay a penny more for their travel in 2020 than they do today".