Recent experiments have measured collisional frequency shifts in polarized fermionic alkaline-earth atoms using 1S0-3P0 Rabi spectroscopy. Here, we provide a first-principles nonequilibrium theoretical description of the interaction frequency shifts starting from the microscopic many-body Hamiltonian. Our formalism describes the dependence of the frequency shift on excitation inhomogeneity, interactions, temperature, and many-body dynamics, provides a fundamental understanding of the effects of the measurement process, and explains the observed density shift data.