Gamma-ray-loud X-ray binaries are binary systems that show non-thermal broadband emission from radio to gamma rays. If the system comprises a massive star and a young non-accreting pulsar, their winds will collide producing broadband non-thermal emission, most likely originated in the shocked pulsar wind. Thermal X-ray emission is expected from the shocked stellar wind, but until now it has neither been detected nor studied in the context of gamma-ray binaries. We present a semi-analytic model of the thermal X-ray emission from the shocked stellar wind in pulsar gamma-ray binaries, and find that the thermal X-ray emission increases monotonically with the pulsar spin-down luminosity, reaching luminosities of the order of 1033 erg s--1. The lack of thermal features in the X-ray spectrum of gamma-ray binaries can then be used to constrain the properties of the pulsar and stellar winds. By fitting the observed X-ray spectra of gamma-ray binaries with a source model composed of an absorbed non-thermal power law and the computed thermal X-ray emission, we are able to derive upper limits on the spin-down luminosity of the putative pulsar. We applied this method to LS 5039, the only gamma-ray binary with a radial, powerful wind, and obtain an upper limit on the pulsar spin-down luminosity of ~6 X 1036 erg s--1. Given the energetic constraints from its high-energy gamma-ray emission, a non-thermal to spin-down luminosity ratio very close to unity may be required.