Cenozoic global climate and the marine carbon cycle exhibit synchronized variations on the astronomical rhythms of 405,000- and 100,000-year eccentricity cycles. Here, we explore the in-phase interactions between climate and the carbon cycle through a multi-proxy reconstruction that includes benthic foraminiferal stable oxygen and carbon isotopes, carbonate ion saturation inferred from boron-to-calcium ratios, and calcium carbonate content. We report a discrepancy between the eccentricity pacing of carbonate dissolution cycles and deep-water carbonate ion saturation. To reconcile this, we argue, based on biogeochemical modelling, that carbonate burial along continental shelves plays a dominant role in altering carbonate ion concentrations and is sufficient to drive changes in seawater carbon isotope on eccentricity timescales. This mechanism is intimately linked to the transport of dissolved inorganic carbon and alkalinity via monsoon rainfall and chemical weathering, suggesting that low-latitude climate processes amplify the influence of eccentricity on the oceanic carbon cycle, particularly in an ice-free, unipolar glacial world.