He succeeded throne of Phaltan after his father Naik Nimbalkar Mudhoji II. He was sixteenth direct descent from Padakla Jagdevrao Parmar, the founder of his dynasty and Phaltan. Bajaji was the brother-in-law of Shivaji, the founder of Maratha Empire, as his sister Maharani Saibai was his first wife. His sons were Mahadaji and Vanangoji. Mahadaji married Sakhubai, the eldest daughter of Shivaji and Saibai.
He fought many battles for sultans of Deccan and for Marathas. However, it is said that he embraced the Muslim religion after Adilshah's pressure to join Islam. Later, Shivaji brought him in Hindu religion at Nira-Narsingpur and he had given his daughter to Bajaji's Son. Bajaji also married to Ahirekar Patil and Bhosale Kinhaikar's daughters when returning to Hindu religion.