This paper introduces an innovative unified deep learning (DL) model, “reduced deep convolutional stack autoencoder (RDCSAE)-robust kernel-based random vector functional link network (RKRVFLN)” (RDCSAE-RKRVFLN), for addressing practical challenges like phase and gain uncertainty, mutual coupling effects, and element position errors in direction of arrival (DOA) estimation. The RDCSAE utilizes deep convolutional neural network (DCNN) and stack autoencoder (SAE) for robust feature extraction. The RKRVFLN integrates a concise SAE output with kernel-based learning. Thus, the integration of RDCSAE (suitable for unsupervised feature extraction) and RKRVFLN (for supervised learning) in the developed model results in efficient use of limited training data. Performance metrics of this method include among others the accuracy (separation between sources), root mean square error (RMSE), signal-to-noise ratio (SNR), etc. The method performs better than existing data driven methods in terms of computational efficiency, faster learning speed, enhanced model generalization, higher accuracy, and shorter event regression time and empirical methods. In the presence of above mentioned four perturbations, this method successfully resolves multiple sources with a resolution of 0.3° with a RMSE of 0.00376. For real time application, the paper implements RDCSAE-RKRVFLN on a high-speed reconfigurable Xilinx Virtex-5 field-programmable gate array (FPGA) realizing a digital DOA estimator for one source. The hardware estimates the DOA with a maximum error of 0.01953125 which follows closely the simulation results indicating the efficiency and feasibility of the method.