Gulabchand Kataria, Rajasthan's home minister, said: "It was a low intensity explosion. Preliminary information suggests a lunch box appeared to be packed with something which exploded."
Sayeed Tariq, an eyewitness, told reporters the blast triggered mayhem in the narrow ally that leads to the shrine.
"There was a stampede as people shouted 'bomb, bomb' and ran from the shrine," he said.
Police sealed the area after the blast, and explosives experts were sent to the area.
Markets in the town quickly closed after the blasts.
Chishti, the saint, is known as the benefactor of the poor, and his shrine, like many sufi monuments in India, attracts people of all faiths, who go there to make a wish.
No one immediately claimed responsibility for the explosion, but The Press Trust of India quoted unnamed federal government officials as labelling the Ajmer blast a "terror strike" staged by anti-Indian fighters.