We present a method for the direct measurement of the Wigner characteristic function of a thermalizing harmonic oscillator that is completely inaccessible for control or measurement. The strategy employs a recently proposed probe-measurement-based scheme [Phys. Rev. Lett. 122, 110406 (2019), 10.1103/PhysRevLett.122.110406] which relies on the pulsed control of a two-level probe. We generalize this scheme to the case of a nonunitary time evolution of the target harmonic oscillator, describing its thermalization through contact to a finite-temperature environment, given in the form of a Lindblad master equation. This generalization is achieved using a superoperator formalism and yields analytical expressions for the direct measurement of the characteristic function, accounting for the decoherence during the measurement process.