A general and robust Bayesian optimization framework for the extraction of intrinsic physical properties from an integration of pore-scale forward modeling and experimental measurements of macroscopic system responses is developed. The efficiency of the scheme, which utilizes Gaussian process regression, enables the simultaneous extraction of multiple intrinsic physical properties with a minimal number of function evaluations. Here it is applied to nuclear magnetic resonance (NMR) relaxation responses, paving the way for inverse problem approaches to digital rock physics given its general nature. NMR relaxation responses of fluids in porous media may be described by sums of multiexponential decays resulting in a relaxation time distribution. The shape of this distribution is dependent on intrinsic physical system properties, but also effects like diffusion coupling between different relaxation regimes in heterogeneous porous materials. Forward models based on high-resolution images are employed to naturally incorporate structural heterogeneity and diffusive motion without limiting assumptions. Extracting the required multiple intrinsic parameters of the system poses an ill-conditioned multiphysics multiparameter inverse problem where multiple scales are covered by the underlying microstructure. Exploration of the multidimensional search space given an expensive cost function makes an efficient solution strategy mandatory. We propose a workflow to match experimental measurements with simulations via Bayesian optimization, with special attention paid to the multimodal nature of the topography of the objective function using solution space partitioning. A multimodal search strategy using state-of-the-art evolutionary algorithms and gradient-based optimization algorithms guarantees that the multimodal nature is captured. The workflow is demonstrated on ${T}_{2}$ relaxation responses of Bentheimer sandstone, extracting three physical parameters simultaneously: the surface relaxivity of quartz grains, the effective transverse relaxation time, and the effective diffusion coefficient in clay regions. Multiple mathematically sound and physically plausible solutions corresponding to global minimum and multiple local minima of the objective function are identified within a limited number of function evaluations. Importantly, the shape of the experimental ${T}_{2}$ distribution is recovered almost perfectly, enabling the use of classical interpretation techniques and local analysis of responses based on numerical simulation.