Zardari announced the donation, which the shrine's administrators have described as one of the biggest in recent years, when he offered prayers at the dargah on April 8.
The President visited the shrine in Rajasthan after meeting Prime Minister Manmohan Singh during a day-long private visit to India.
Presidential spokesman Babar told The News daily that the donation for the shrine in Ajmer will be paid from public money.
A cheque for USD 50,000 handed over by Zardari to the administrators of Mughal emperor Bahadur Shah Zafar's mausoleum in Yangon too was paid from the exchequer, Babar said.
It could not immediately be ascertained when the donation would be handed over to the administrators of the shrine in Ajmer, which has been visited by several Pakistani leaders, including Zardari's slain wife, former premier Benazir Bhutto.