Lee won a High Court defamation case against blogger Roy Ngerng, 33, in November, the first time the city-state's leader sued an online critic.
Ngerng was sued for his blog post in May when he was alleged to have implicated Lee in impropriety in connection with how funds in Singapore's mandatory retirement savings scheme, the Central Provident Fund(CPF), are managed.
Ngerng was ordered to pay the amount for legal fees and related expenses, Chang Li Lin, the press secretary to the prime minister said in a statement.
She said said the dates for the subsequent hearings - which will determine the amount of damages payable to Lee - are not confirmed.
"At the hearing today, the judge ordered that the total costs to be paid by the defendant to the plaintiff be fixed at S$29,000," she said.
"This amount is for the legal fees and related expenses incurred up to the conclusion of the application for summary judgement."
Singapore's leaders have in the past sued or settled out of court with several foreign media publications including The New York Times, Wall Street Journal, Bloomberg and The Economist for alleged defamatory remarks but this is the first time a blogger has faced such action.