He was a professor at the Centre for Advanced Studies in Medieval History at his alma mater, Aligarh Muslim University.

His oldest son, Taimur Athar is a renowned research scientist at the Indian Institute of Chemical Technology in Hyderabad, Telangana.

The book led to a reconsideration of many standard views of the ethnic composition of the Mughal ruling class and was widely regarded as a strong critique of communalist historiography in India and Pakistan.

The theory, which still receives support from many quarters, that Aurangazeb's "religious bias" generated a "Hindu backlash" which brought about the downfall of the empire, was challenged by Ali on the basis of hard evidence.

"The evidence I assembled," wrote Ali in his introduction to the revised edition of the book, "did not in any sense exonerate Aurangazeb, but I think it did set different limits within which the Emperor's personal preferences and decisions had impact: and it suggested a number of other factors, besides the one of religious bias..." In 1985, Ali published his second major work, The Apparatus of Empire: Awards of Ranks, Offices and Titles to the Mughal Nobility, 1574-1658.

In his introduction to the work's extensive tables, Ali demonstrated how the quantitative data obtained from them could tell the reader the internal processes of the Mughal polity.