Machado de Assis wrote nine novels, according to the bibliography of the Brazilian Academy of Letters, in addition to about two hundred stories, poetry, drama, and more than six hundred chronicles.
The nine novels are, in order of publication: Resurrection (1872), The Hand and the Glove (1874), Helena (1876), Iaiá Garcia (1878), The Posthumous Memoirs of Brás Cubas (1881), Quincas Borba (1891), Dom Casmurro (1899), Esau and Jacob (1904), and Counselor Ayres' Memorial (1908). Wikipedia speaks of ten novels, which shows that the count depends on the criterion adopted for what counts as a novel.
The stories came out in collections such as Contos Fluminenses (1870), Midnight Stories (1873), Loose Papers (1882), Undated Stories (1884), Various Stories (1896), and Relics of an Old House (1906). The total varies according to the source: Wikipedia itself gives 205 stories at the outset, citing the Dictionary of Machado de Assis by Ubiratan Machado, and 219 in another passage.
In poetry, he published Crisálidas (1864), Falenas (1870), Americanas (1875), and Ocidentais (1901), gathered in the Poesias Completas (1901). Wikipedia also adds ten plays.
On Clavis: The Posthumous Memoirs of Brás Cubas, Quincas Borba.