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Many key environmental, industrial, and energy processes rely on controlling fluid transport within subsurface porous media. These media are typically structurally heterogeneous, often with vertically-layered strata of distinct permeabilities—leading to uneven partitioning of flow across strata, which can be undesirable. Here, using direct in situ visualization, we demonstrate that polymer additives can homogenize this flow by inducing a purely- elastic flow instability that generates random spatiotemporal fluctuations and excess flow resistance in individual strata. In particular, we find that this instability arises at smaller imposed flow rates in higher-permeability strata, diverting flow towards lower-permeability strata and helping to homogenize the flow. Guided by the experiments, we develop a parallel-resistor model that quantitatively predicts the flow rate at which this homogenization is optimized for a given stratified medium. Thus, our work provides a new approach to homogenizing fluid and passive scalar transport in heterogeneous porous media.