Although the baryons in the intergalactic medium (IGM) trace dark matter fluctuations on megaparsec scales, on smaller scales ∼100 kpc, fluctuations are suppressed because the finite temperature gas is pressure supported against gravity, analogous to the classical Jeans argument. This Jeans filtering scale, which quantifies the small-scale structure of the IGM, has fundamental cosmological implications. First, it provides a thermal record of heat injected by ultraviolet photons during cosmic reionization events, and thus constrains the thermal and reionization history of the universe. Second, the Jeans scale determines the clumpiness of the IGM, a critical ingredient in models of cosmic reionization. Third, it sets the minimum mass scale for gravitational collapse from the IGM, and hence plays a pivotal role in galaxy formation. Unfortunately, it is extremely challenging to measure the Jeans scale via the standard technique of analyzing purely longitudinal Lyα forest spectra, because the thermal Doppler broadening of absorption lines along the line-of-sight, is highly degenerate with Jeans smoothing. In this work, we show that the Jeans filtering scale can be directly measured by characterizing the coherence of correlated Lyα forest absorption in close quasar pairs, with separations small enough ∼100 kpc to resolve it. We present a novel technique for this purpose, based on the probability density function (PDF) of phase angle differences of homologous longitudinal Fourier modes in close quasar pair spectra. A Bayesian formalism is introduced based on the phase angle PDF, and Markov Chain Monte Carlo techniques are used to characterize the precision of a hypothetical Jeans scale measurement, and explore degeneracies with other thermal parameters governing the IGM. A semi-analytical model of the Lyα forest is used to generate a large grid (500) of thermal models from a dark matter only simulation. Our full parameter study indicates that a realistic sample of only 20 close quasar pair spectra can pinpoint the Jeans scale to ≃ 5% precision, independent of the amplitude T 0 and slope γ of the temperature-density relation of the IGM . This exquisite sensitivity arises because even long-wavelength one-dimensional Fourier modes ∼10 Mpc, i.e., two orders of magnitude larger than the Jeans scale, are nevertheless dominated by projected small-scale three-dimensional (3D) power. Hence phase angle differences between all modes of quasar pair spectra actually probe the shape of the 3D power spectrum on scales comparable to the pair separation. We show that this new method for measuring the Jeans scale is unbiased and is insensitive to a battery of systematics that typically plague Lyα forest measurements, such as continuum fitting errors, imprecise knowledge of the noise level and/or spectral resolution, and metal-line absorption. © 2013. The American Astronomical Society. All rights reserved..