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Quantum decoherence is the disappearance of simple phase relations within a discrete quantum system as a result of interactions with an environment. For many applications, the question is not necessarily how to avoid (inevitable) system-environment interactions, but rather how to design environments that optimally preserve a system's phase relations in spite of such interactions. The formation of system-environment entanglement is a major driving mechanism for decoherence, and a detailed understanding of this process could inform strategies for conserving coherence optimally. This requires scalable, flexible, and systematically improvable quantum dynamical methods that retain detailed information about the entanglement properties of the environment, yet very few current methods offer this combination of features. Here, we address this need by introducing a theoretical framework wherein we combine the truncated Wigner approximation with standard time-dependent perturbation theory allowing for computing expectation values of operators in the combined system-environment Hilbert space. We demonstrate the utility of this framework by applying it to the spin-boson model, representative of qubits and simple donor-acceptor systems. For this model, our framework provides an analytical description of perturbative contributions to expectation values. We monitor how quantum decoherence at zero temperature is accompanied by entanglement formation with individual environmental degrees of freedom. Based on this entanglement behavior, we find that the selective suppression of low-frequency environmental modes is particularly effective for mitigating quantum decoherence.