In recent years, significant advancements in artificial intelligence, particularly in the field of deep learning, have increasingly been integrated into agricultural applications, including critical processes such as disease detection. Tomato, being one of the most widely consumed agricultural products globally and highly susceptible to a variety of fungal, bacterial, and viral pathogens, remains a prominent focus in disease detection research. In this study, we propose a deep learning-based approach for the detection of tomato diseases, a critical challenge in agriculture due to the crop’s vulnerability to fungal, bacterial, and viral pathogens. We constructed an original dataset comprising 6414 images captured under real production conditions, categorized into three image types: leaves, green tomatoes, and red tomatoes. The dataset includes five classes: healthy samples, late blight, early blight, gray mold, and bacterial cancer. Twenty-one deep learning models were evaluated, and the top five performers (EfficientNet-b0, NasNet-Large, ResNet-50, DenseNet-201, and Places365-GoogLeNet) were selected for feature extraction. From each model, 1000 deep features were extracted, and feature selection was conducted using MRMR, Chi-Square (Chi2), and ReliefF methods. The top 100 features from each selection technique were then used for reclassification with traditional machine learning classifiers under five-fold cross-validation. The highest test accuracy of 92.0% was achieved with EfficientNet-b0 features, Chi2 selection, and the Fine KNN classifier. EfficientNet-b0 consistently outperformed other models, while the combination of NasNet-Large and Wide Neural Network yielded the lowest performance. These results demonstrate the effectiveness of combining deep learning-based feature extraction with traditional classifiers and feature selection techniques for robust detection of tomato diseases in real-world agricultural environments.