Benchmark-based evaluation, e.g., multiple-choice questions (MCQs) and open-ended questions (OEQs), is widely used for evaluating Large Language Models (LLMs), yet their reliability is undermined by benchmark contamination. When pre-exposed to the testing benchmark during training, less capable LLMs have been found to achieve inflated performance, thereby yielding erroneous results in LLM evaluation. In this study, we reframe contamination as an inherent aspect of learning and seek to disentangle and expose genuine capability acquisition from superficial memorization in LLM evaluation. Following this, firstly, by analyzing model performance under different memorization conditions of MCQs, we uncover a counterintuitive trend: LLMs perform worse on memorized benchmarks than on non-memorized ones, indicating the coexistence of two learning phenomena, i.e., rote memorization and genuine capability learning. To disentangle them, we propose TrinEval, a novel evaluation framework that reformulates MCQs into an alternative knowledge-centric trinity format, reducing memorization while preserving inherent knowledge, enabling the evaluation of genuine capability in the presence of memorization. Extensive experiments validate the effectiveness and robustness of TrinEval in reformulating benchmarks, and the evaluation results further reveal that mainstream LLMs rely on rote memorization for an average of 19.6% of knowledge points across the MMLU and the GSM8K dataset.