High-precision habitat mapping can contribute to the identification and quantification of the human footprint on the seafloor. As a representative of seafloor habitats, seabed sediment classification is crucial for marine geological research, marine environment monitoring, marine engineering construction, and seabed biotic and abiotic resource assessment. Multibeam echo-sounding systems (MBES) have become the most popular tool in terms of acoustic equipment for seabed sediment classification. However, sonar images tend to consist of obvious noise and stripe interference. Furthermore, the low efficiency and high cost of seafloor field sampling leads to limited field samples. The factors above restrict high accuracy classification by a single classifier. To further investigate the classification techniques for seabed sediments, we developed a decision fusion algorithm based on voting strategies and fuzzy membership rules to integrate the merits of deep learning and shallow learning methods. First, in order to overcome the influence of obvious noise and the lack of training samples, we employed an effective deep learning framework, namely random patches network (RPNet), for classification. Then, to alleviate the over-smoothness and misclassifications of RPNet, the misclassified pixels with a lower fuzzy membership degree were rectified by other shallow learning classifiers, using the proposed decision fusion algorithm. The effectiveness of the proposed method was tested in two areas of Europe. The results show that RPNet outperforms other traditional classification methods, and the decision fusion framework further improves the accuracy compared with the results of a single classifier. Our experiments predict a promising prospect for efficiently mapping seafloor habitats through deep learning and multi-classifier combinations, even with few field samples.