In the band theory for non-Hermitian systems, the energy eigenvalues, which are complex, can exhibit non-trivial topology which is not present in Hermitian systems. In one dimension, it was recently noted theoretically and demonstrated experimentally that the eigenvalue topology is classified by the braid group. The classification of eigenvalue topology in higher dimensions, however, remained an open question. Here, we give a complete description of eigenvalue topology in two and three dimensional systems, including the gapped and gapless cases. We reduce the topological classification problem to a purely computational problem in algebraic topology. In two dimensions, the Brillouin zone torus is punctured by exceptional points, and each nontrivial loop in the punctured torus acquires a braid group invariant. These braids satisfy the constraint that the composite of the braids around the exceptional points is equal to the commutator of the braids on the fundamental cycles of the torus. In three dimensions, there are exceptional knots and links, and the classification depends on how they are embedded in the Brillouin zone three-torus. When the exceptional link is contained in a contractible ball, the classification can be expressed in terms of the knot group of the link. Our results provide a comprehensive understanding of non-Hermitian eigenvalue topology in higher dimensional systems, and should be important for the further explorations of topologically robust open quantum and classical systems.