This paper introduces essential resources for Qur'anic studies: an annotated Tafsir ontology, a dataset of approximately 4,200 question-answer pairs, and a collection of 15 structured Tafsir books available in two formats. We present a comprehensive framework for handling sensitive Qur'anic Tafsir data that spans the entire pipeline from dataset construction through evaluation and error analysis. Our work establishes new benchmarks for retrieval and question-answering tasks on Qur'anic content, comparing performance across state-of-the-art embedding models and large language models (LLMs). We introduce OntologyRAG-Q, a novel retrieval-augmented generation approach featuring our custom Ayat-Ontology chunking method that segments Tafsir content at the verse level using ontology-driven structure. Benchmarking reveals strong performance across various LLMs, with GPT-4 achieving the highest results, followed closely by ALLaM. Expert evaluations show our system achieves 69.52\% accuracy and 74.36\% correctness overall, though multi-hop and context-dependent questions remain challenging. Our analysis demonstrates that answer position within documents significantly impacts retrieval performance, and among eleven evaluation metrics tested, BERT-recall and BERT-F1 correlate most strongly with expert assessments. All resources developed in this study will be publicly available at \url{https://github.com/OntologyRAG-Q/OntologyRAG-Q.git}.