This study presents a comprehensive deep learning pipeline for the automated classification of foraminifera species using 2D micro-CT slices derived from 3D scans. We curated a scientifically rigorous dataset of 97 micro-CT scanned specimens spanning 27 species, from which we selected 12 representative species with sufficient specimen counts (at least four 3D models each) for robust classification. To ensure methodological integrity and prevent data leakage, we employed specimen-level data splitting, resulting in 109,617 high-quality 2D slices (44,103 for training, 14,046 for validation, and 51,468 for testing). We evaluated seven state-of-the-art 2D convolutional neural network (CNN) architectures using transfer learning. Our final ensemble model, ForamDeepSlice (FDS), combining ConvNeXt-Large and EfficientNetV2-Small, achieved a test accuracy of 95.64%, with a top-3 accuracy of 99.6% and an area under the ROC curve (AUC) of 0.998 across all species. To facilitate practical deployment, we developed an interactive advanced dashboard that supports real-time slice classification and 3D slice matching using advanced similarity metrics, including SSIM, NCC, and the Dice coefficient. This work establishes new benchmarks for AI-assisted micropaleontological identification and provides a fully reproducible framework for foraminifera classification research, bridging the gap between deep learning and applied geosciences.