Du Toit, who was born at Rondebosch, near Cape Town in South Africa, studied at the South Africa College (now the University of Cape Town), the Royal Technical College, Glasgow, and the Royal College of Science, London.

After a short period teaching at Glasgow University (1901–03) he returned to South Africa and worked with the Geological Commission of the Cape of Good Hope (1903–20), during which he explored the geology of South Africa. For the next seven years he worked for the Irrigation Department and produced six detailed monographs on South African geology. He served as a consulting geologist to De Beers Consolidated Mines during the period 1927–41.

Following a visit to South America in 1923, du Toit became one of the earliest supporters of Alfred Wegener's theory of continental drift, publishing his observations in A Geological Comparison of South America with South Africa (1927). He noted the similarity between the continents and developed his ideas in Our Wandering Continents (1937), in which he argued for the separation of Wegener's Pangaea into the two supercontinents, Laurasia and Gondwanaland.