Zeroth-order (ZO) optimization has emerged as a promising alternative to gradient-based backpropagation methods, particularly for black-box optimization and large language model (LLM) fine-tuning. However, ZO methods suffer from slow convergence due to high-variance stochastic gradient estimators. While structured perturbations, such as sparsity and low-rank constraints, have been explored to mitigate these issues, their effectiveness remains highly under-explored. In this work, we develop a unified theoretical framework that analyzes both the convergence and generalization properties of ZO optimization under structured perturbations. We show that high dimensionality is the primary bottleneck and introduce the notions of \textit{stable rank} and \textit{effective overlap} to explain how structured perturbations reduce gradient noise and accelerate convergence. Using the uniform stability under our framework, we then provide the first theoretical justification for why these perturbations enhance generalization. Additionally, through empirical analysis, we identify that \textbf{block coordinate descent} (BCD) to be an effective structured perturbation method. Extensive experiments show that, compared to existing alternatives, memory-efficient ZO (MeZO) with BCD (\textit{MeZO-BCD}) can provide improved converge with a faster wall-clock time/iteration by up to $\times\textbf{2.09}$ while yielding similar or better accuracy.