Thomas Jones Mackie was educated at the Hamilton Academy and continued his studies at the University of Glasgow. He was awarded the degrees Bachelor of Medicine (MB) and Bachelor in Surgery (ChB) with honours in 1910 and received the Brunton Memorial Prize as the best student of his year. For a short time he worked as house-surgeon and house-physician at the Glasgow Western Infirmary and then was awarded a Carnegie Scholarship which enabled him to become a research scholar and fellow in pathology in the university's Department of Pathology from 1911 to 1914. He obtained the Oxford Diploma in Public Health in 1913 and worked as an assistant at the Bland-Sutton Institute of Pathology at the Middlesex Hospital and Medical School, London, in 1914. When World War I (1914-1918) broke out he was attached to the Royal Army Medical Corps, serving mainly in the Middle East, and was appointed to the command of the Central Bacteriological Laboratory in Alexandria, Egypt, with the rank of captain.
At the conclusion of the war in 1918 Mackie was appointed as the Wernher-Beit professor of bacteriology at the University of Cape Town. While there he was awarded the degree Doctor of Medicine (MD) by the University of Glasgow in 1921. Despite the fact that he did much routine diagnostic work for New Somerset Hospital he was an active researcher. He was elected a Fellow of the Royal Society of South Africa in 1920, was elected a member of its council for 1923, and published several papers on immunity and syphilis in the society's Transactions: 'Haemolysis by serum in combination with certain benzol bodies' (1919/20, Vol. 8), 'A study of the B.col group with special reference to the serological characters of these organisms' (1921, Vol. 9), 'Observations on the protective action of normal serum in experimental infection with Bacillus Diphtheria' (1922, Vol. 10), and 'The serum constituents responsible for the Sachs-Georgi and Wasserman reactions' (1924, Vol. 11). He also completed a booklet, Bacteriological methods (University of Cape Town, 1922, 39 pp.) and was one of the chief planners of a full medical school at the university.
In 1923 Mackie accepted an appointment as professor of bacteriology at the University of Edinburgh, a post he held to his death in 1955. From 1953 he served as dean of the Faculty of Medicine. During this period he wrote An introduction to practical bacteriology as applied to medicine and public health (with J.E. McCartney. Edinburgh, 1925; 9th ed. with changed title, 1953). He also continued publishing a total of some ninety papers in bacteriology, in journals such as The Journal of Hygiene, British Journal of Experimental Pathology, Journal of Comparative Pathology and Therapeutics, and The Lancet.
Mackie also served as honorary bacteriologist and senior consultant in bacteriology at the Royal Infirmary of Edinburgh, council member of the Lister Institute of Preventive Medicine, member of the Scientific Advisory Committee of the Department of Health for Scotland and chairman of its Infectious Diseases Subcommittee, member of the Agricultural Research Council, director of the Animal Diseases Research Association of Scotland, chairman of the Scottish Hill Farm Research Committee, and as examiner for several universities. In recognition of his work he was honoured as Commander of the Order of the British Empire (CBE) in 1942. The University of Glasgow awarded him an honorary Doctor of Laws degree in 1947. He was admitted as a Member of the Royal College of Physicians of Edinburgh and elected a Fellow of the Royal Society of Edinburgh.
Mackie was married to Edith Warner, with whom he had a son and a daughter.