Optimal prompt selection is crucial for maximizing large language model (LLM) performance on downstream tasks. As the most powerful models are proprietary and can only be invoked via an API, users often manually refine prompts in a black-box setting by adjusting instructions and few-shot examples until they achieve good performance as measured on a validation set. Recent methods addressing static black-box prompt selection face significant limitations: They often fail to leverage the inherent structure of prompts, treating instructions and few-shot exemplars as a single block of text. Moreover, they often lack query-efficiency by evaluating prompts on all validation instances, or risk sub-optimal selection of a prompt by using random subsets of validation instances. We introduce HbBoPs, a novel Hyperband-based Bayesian optimization method for black-box prompt selection addressing these key limitations. Our approach combines a structural-aware deep kernel Gaussian Process to model prompt performance with Hyperband as a multi-fidelity scheduler to select the number of validation instances for prompt evaluations. The structural-aware modeling approach utilizes separate embeddings for instructions and few-shot exemplars, enhancing the surrogate model's ability to capture prompt performance and predict which prompt to evaluate next in a sample-efficient manner. Together with Hyperband as a multi-fidelity scheduler we further enable query-efficiency by adaptively allocating resources across different fidelity levels, keeping the total number of validation instances prompts are evaluated on low. Extensive evaluation across ten benchmarks and three LLMs demonstrate that HbBoPs outperforms state-of-the-art methods.