We study diffusion-controlled two-species annihilation with a finite number of particles. In this stochastic process, particles move diffusively, and when two particles of opposite type come into contact, the two annihilate. We focus on the behavior in three spatial dimensions and for initial conditions where particles are confined to a compact domain. Generally, one species outnumbers the other, and we find that the difference between the number of majority and minority species, which is a conserved quantity, controls the behavior. When the number difference exceeds a critical value, the minority becomes extinct and a finite number of majority particles survive, while below this critical difference, a finite number of particles of both species survive. The critical difference Δ_{c} grows algebraically with the total initial number of particles N, and when N≫1, the critical difference scales as Δ_{c}∼N^{1/3}. Furthermore, when the initial concentrations of the two species are equal, the average number of surviving majority and minority particles, M_{+} and M_{-}, exhibit two distinct scaling behaviors, M_{+}∼N^{1/2} and M_{-}∼N^{1/6}. In contrast, when the initial populations are equal, these two quantities are comparable M_{+}∼M_{-}∼N^{1/3}.