Identifying LLM-generated code through watermarking poses a challenge in preserving functional correctness. Previous methods rely on the assumption that watermarking high-entropy tokens effectively maintains output quality. Our analysis reveals a fundamental limitation of this assumption: syntax-critical tokens such as keywords often exhibit the highest entropy, making existing approaches vulnerable to logic corruption. We present STONE, a syntax-aware watermarking method that embeds watermarks only in non-syntactic tokens and preserves code integrity. For rigorous evaluation, we also introduce STEM, a comprehensive metric that balances three critical dimensions: correctness, detectability, and imperceptibility. Across Python, C++, and Java, STONE preserves correctness, sustains strong detectability, and achieves balanced performance with minimal computational overhead. Our implementation is available at https://github.com/inistory/STONE-watermarking.