With the rapid expansion of intelligent resource-constrained devices and high-speed communication technologies, Internet of Things (IoT) has earned a wide recognition as the primary standard for low-power lossy networks (LLNs). Nevertheless, IoT infrastructures are vulnerable to cyber-attacks due to the constraints in computation, storage, and communication capacity of the endpoint devices. From one side, the majority of newly developed cyber-attacks are formed by slightly mutating formerly established cyber-attacks to produce a new attack tending to be treated as a normal traffic through the IoT network. From the other side, the influence of coupling the deep learning techniques with cybersecurity field has become a recent inclination of many security applications due to their impressive performance. In this paper, we provide a comprehensive development of a new intelligent and autonomous deep learning-based detection and classification system for cyber-attacks in IoT communication networks leveraging the power of convolutional neural networks, abbreviated as (IoT-IDCS-CNN). The proposed IoT-IDCS-CNN makes use of the high-performance computing employing the robust CUDA based Nvidia GPUs and the parallel processing employing the high-speed I9-Cores based Intel CPUs. In particular, the proposed system is composed of three subsystems: Feature Engineering subsystem, Feature Learning subsystem and Traffic classification subsystem. All subsystems are developed, verified, integrated, and validated in this research. To evaluate the developed system, we employed the NSL-KDD dataset which includes all the key attacks in the IoT computing. The simulation results demonstrated more than 99.3% and 98.2% of cyber-attacks’ classification accuracy for the binary-class classifier (normal vs anomaly) and the multi-class classifier (five categories) respectively. The proposed system was validated using k-fold cross validation method and was evaluated using the confusion matrix parameters (i.e., TN, TP, FN, FP) along with other classification performance metrics including precision, recall, F1-score, and false alarm rate. The test and evaluation results of the IoT-IDCS-CNN system outperformed many recent machine-learning based IDCS systems in the same area of study.