We compute the topological susceptibility $chi_t$ of lattice QCD with $2+1$ dynamical quark flavors described by the Mobius domain wall fermion. Violation of chiral symmetry as measured by the residual mass is kept at $sim$1 MeV or smaller. We measure the fluctuation of the topological charge density in a `slab sub-volume of the simulated lattice using the method proposed by Bietenholz {it et al.} The quark mass dependence of $chi_t$ is consistent with the prediction of chiral perturbation theory, from which the chiral condensate is extracted as $Sigma^{overline{rm MS}} (mbox{2GeV}) = [274(13)(29)mbox{MeV}]^3$, where the first error is statistical and the second one is systematic. Combining the results for the pion mass $M_pi$ and decay constant $F_pi$, we obtain $chi_t = 0.229(03)(13)M_pi^2F_pi^2$ at the physical point.