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Both President Zardari and his son Bilawal Bhutto laid 'chadars' at the Mazar.
"The soulful happiness that I have experienced at this holy place is beyond explanation. I pray to Allah to make life easy for the entire humanity," President Zardari wrote in a diary at the shrine.
He landed in the city in a chopper soon after 4 pm on Sunday after a lunch with Prime Minister Manmohan Singh and several other leaders in New Delhi.
Accompanying the president in his Ajmer visit was his 23-year-old son Bilawal Bhutto Zardari. Zardari last visited Ajmer in 2005 with his wife Benazir Bhutto.