Advanced Persistent Threats (APTs) pose a major cybersecurity challenge due to their stealth and ability to mimic normal system behavior, making detection particularly difficult in highly imbalanced datasets. Traditional anomaly detection methods struggle to effectively differentiate APT-related activities from benign processes, limiting their applicability in real-world scenarios. This paper introduces APT-LLM, a novel embedding-based anomaly detection framework that integrates large language models (LLMs) -- BERT, ALBERT, DistilBERT, and RoBERTa -- with autoencoder architectures to detect APTs. Unlike prior approaches, which rely on manually engineered features or conventional anomaly detection models, APT-LLM leverages LLMs to encode process-action provenance traces into semantically rich embeddings, capturing nuanced behavioral patterns. These embeddings are analyzed using three autoencoder architectures -- Baseline Autoencoder (AE), Variational Autoencoder (VAE), and Denoising Autoencoder (DAE) -- to model normal process behavior and identify anomalies. The best-performing model is selected for comparison against traditional methods. The framework is evaluated on real-world, highly imbalanced provenance trace datasets from the DARPA Transparent Computing program, where APT-like attacks constitute as little as 0.004\% of the data across multiple operating systems (Android, Linux, BSD, and Windows) and attack scenarios. Results demonstrate that APT-LLM significantly improves detection performance under extreme imbalance conditions, outperforming existing anomaly detection methods and highlighting the effectiveness of LLM-based feature extraction in cybersecurity.