This work studies the problem of jointly estimating unknown parameters from Kronecker-structured multidimensional signals, which arises in applications like intelligent reflecting surface (IRS)-aided channel estimation. Exploiting the Kronecker structure, we decompose the estimation problem into smaller, independent subproblems across each dimension. Each subproblem is posed as a sparse recovery problem using basis expansion and solved using a novel off-grid sparse Bayesian learning (SBL)-based algorithm. Additionally, we derive probabilistic error bounds for the decomposition, quantify its denoising effect, and provide convergence analysis for off-grid SBL. Our simulations show that applying the algorithm to IRS-aided channel estimation improves accuracy and runtime compared to state-of-the-art methods through the low-complexity and denoising benefits of the decomposition step and the high-resolution estimation capabilities of off-grid SBL.