Zanabazar was born in 1635, a son of the Tusheet Khan Gombodorj, one of the great princes of Khalkha Mongolia and a descendant of Chinggis. As a small child he was acclaimed by the Khalkha nobles as their religious head, and in the following years he travelled to Tibet, where the fifth Dalai Lama and the Panchen Lama confirmed him as the rebirth of Taranatha, the Jonang historian who had died in Mongolia in 1634. The recognition attached him to the Gelug order rather than to the Jonang, whose institutions were being absorbed at that time, and it is a good example of how an incarnation line can be used to settle an argument between schools.
The title Jebtsundamba Khutuktu made him head of Buddhism in Khalkha and the first of a line that ran to the eighth, who was also the last ruler of independent Mongolia and died in 1924. The combination of religious primacy with Chinggisid descent is why his decisions were political.
The decision that mattered most came in 1688, when the Dzungar leader Galdan invaded Khalkha and drove the population east. Zanabazar led the Khalkha nobles to seek Qing protection, and in 1691 at Dolonnor they submitted to the Kangxi emperor. Khalkha Mongolia remained under Qing rule until 1911. The judgement has been argued about ever since, because it preserved the Khalkha as a people and their monasteries as institutions, and it ended their independence.