A non-Brownian suspension of micron scale rods exhibits reversible shear-driven formation of disordered aggregates resulting in dramatic viscosity enhancement at low shear rates. Aggregate formation is imaged using a combined rheometer and fluorescence microscope. The size and structure of these aggregates are found to be a function of shear rate and concentration, with larger aggregates present at lower shear rates and higher concentrations. Quantitative measurements of the early-stage aggregation process are modeled by collision driven growth of porous structures which suggest that the aggregate density increases with shear rate. This result is combined with a Krieger-Dougherty type constitutive relationship and steady-state viscosity measurements to estimate the intrinsic viscosity of complex structures developed under shear. These results represent a direct, quantitative, experimental demonstration of the association between aggregation and viscosity enhancement for a rod suspension, and demonstrate a way of inferring microscopic geometric properties of a dynamic system through the combination of quantitative imaging and rheology.