Police said the accident took place when the driver of the vehicle, carrying over three dozen pilgrims, was blinded by the headlights of an incoming bus.
"Two children died on the spot. Over a dozen were injured, six of them seriously. Persons with serious injuries have been rushed to a medical college in Agra," Deputy SP Sanjai Kumar said.
The pilgrims were returning to Mangrol village in Dholpur district of Rajasthan after performing parikrama (circumambulation) of the Goverdhan hillock here.
The driver of the tractor, Kamta, fled from the spot after the accident, police added.