Tomato is a major global crop, yet foliar diseases seriously affect yield and quality. Accurate and efficient disease identification techniques are of great significance for ensuring agricultural production safety. To address the limitations of existing methods in feature extraction capability, model complexity, and dependence on large-scale labeled data, as well as the difficulty of recognizing early-stage diseases whose visual symptoms are not yet fully developed, this paper proposes SAEFormer, a lightweight and robust disease recognition model. The model integrates a Multi-scale Selective Fusion Attention Block to enhance the ability to model multi-scale semantic information in lesion areas. In addition, by leveraging a self-supervised loss derived from dense relative localization as an auxiliary regularization term, the model’s generalization ability under limited training data is notably enhanced. To optimize normalization and improve inference efficiency, the RepBN normalization strategy is further adopted, significantly reducing computational cost while maintaining model performance. Experimental results on Dataset A show that SAEFormer achieves a Top-1 accuracy of 87.86% with 24.14 M parameters and 5.35 GFLOPs, demonstrating a favorable balance between recognition accuracy and model complexity. The training curves further indicate stable convergence during model optimization. Ablation experiments validate the complementary contributions of the proposed modules. Moreover, SAEFormer achieves competitive performance in cross-dataset evaluation on Dataset B, indicating its potential adaptability to different data distributions. Overall, SAEFormer provides an efficient approach to tomato leaf disease recognition and shows potential for deployment in precision agriculture applications.