We perform a precise calculation of the chiral condensate in QCD using lattice QCD with 2+1 flavors of dynamical overlap quarks. Up and down quark masses cover a range between 3 and 100 MeV on a 16{3}x48 lattice at a lattice spacing approximately 0.11 fm. At the lightest sea quark mass, the finite volume system on the lattice is in the regime. By matching the low-lying eigenvalue spectrum of the Dirac operator with the prediction of chiral perturbation theory at the next-to-leading order, we determine the chiral condensate in (2+1)-flavor QCD with strange quark mass fixed at its physical value as Sigma;{MS[over ]}(2 GeV)=[242(04)(+19/-18) MeV]{3} where the errors are statistical and systematic, respectively.