He was born at Leipzig. His father, Werner Fabricius, director of music in the church of St. Paul at Leipzig, was the author of several works, the most important being Deliciae Harmonicae (1656). The son received his early education from his father, who on his deathbed recommended him to the care of the theologian Valentin Alberti.
He studied under J.G. Herrichen, and afterwards at Quedlinburg under Samuel Schmid. It was in Schmid’s library, as he afterwards said, that he found the two books, Kaspar von Barth's compendium Adversariorum libri LX (1624) and Daniel Georg Morhof's Polyhistor (1688), which suggested to him the idea of his Bibliothecæ, the kind of works on which his great reputation was ultimately founded.
Having returned to Leipzig in 1686, he published anonymously (two years later) his first work, Scriptorum recentiorum decas, an attack on ten writers of the day. His Decas Decadum, sive plagiariorum et pseudonymorum centuria (1689) is the only one of his works to which he signs the name Faber. He then applied himself to the study of medicine, which, however, he relinquished for that of theology; and having gone to Hamburg in 1693, he proposed to travel abroad, when the unexpected tidings that the expense of his education had absorbed his whole patrimony, and even left him in debt to his trustee, forced him to abandon his project.
He therefore remained at Hamburg in the capacity of librarian to J.F. Mayer. In 1696 he accompanied his patron to Sweden; and on his return to Hamburg, not long afterwards, he became a candidate for the chair of logic and philosophy. The suffrages being equally divided between Fabricius and Sebastian Edzardus, one of his opponents, the appointment was decided by lot in favour of Edzardus; but in 1699 Fabricius succeeded Vincent Placcius in the chair of rhetoric and ethics, a post which he held until his death, refusing invitations to Greifswald, Kiel, Giessen, and Wittenberg. He died at Hamburg.
Fabricius is credited with 128 books, but very many of them were only books which he had edited. One of the most famed and laborious of these is the Bibliotheca Latina (1697, republished in an improved and amended form by JA Ernesti, 1773). The divisions of the compilation are--the writers to the age of Tiberius; thence to that of the Antonines; and thirdly, to the decay of the language; a fourth gives fragments from old authors, and chapters on early Christian literature. A supplementary work was Bibliotheca Latina mediae et infimae Aetatis (1734-1736; supplementary volume by C Schottgen, 1746; ed. Mansi, 1754). His chef-d'oeuvre, however, is the Bibliotheca Graeca (1705-1728, revised and continued by G.C. Harles, 1790—1812), a work which has justly been denominated maximus antiquae eruditionis thesaurus. Its divisions are marked off by Homer, Plato, Jesus, Constantine, and the capture of Constantinople in 1453, while a sixth section is devoted to canon law, jurisprudence and medicine.
Of his remaining works we may mention: Bibliotheca Antiquaria, an account of the writers whose works illustrated Hebrew, Greek, Roman and Christian antiquities (1713); Centifolium Lutheranum, a Lutheran bibliography (1728); Bibliotheca Ecclesiastica (1718). His Codex Apocryphus (1703) is still considered indispensable as an authority on apocryphal Christian literature. The details of the life of Fabricius are to be found in De Vita et Scriptis J.A. Fabricii Commentarius, by his son-in-law, H.S. Reimarus, the well-known editor of Dio Cassius, published at Hamburg, 1737; see also C.F. Bähr in Ersch and Gruber's Allgemeine Encyclopaedie, and J.E. Sandys, Hist. Class. Schol. iii (1908).