In the presence of Lindblad decoherence, i.e. dissipative effects in an open quantum system due to interaction with an environment, we examine the transition probabilities for "mass" and "flavor" eigenstates in the two-level quantum system described by non-Hermitian Hamiltonians with the Lindblad equation, for which the parity-time-reversal (PT) symmetry is conserved. First, the density matrix formalism for PT-symmetric non-Hermitian Hamiltonian systems is developed. It is shown that the Lindblad operators L j are pseudo-Hermitian, namely, ηL j η −1 = L † j with η being a linear and positive-definite metric, and respect the PT symmetry as well. We demonstrate that the generalized density matrix ρ G (t) ≡ ρ(t)η, instead of the normalized density matrix ρ N (t) ≡ ρ(t)/tr [ρ(t)], should be implemented for the calculation of the transition probabilities in accordance with the linearity requirement. Second, the density matrix formalism is used to derive the transition probabilities in general cases of PT-symmetric non-Hermitian Hamiltonians. In some concrete examples, we calculate compact analytical formulas for the transition probabilities and explore their main features with numerical illustrations. We also make a comparison between our present results and our previous ones using state vectors in the absence of Lindblad decoherence.