Deep Kernel Learning (DKL) combines the representational power of neural networks with the uncertainty quantification of Gaussian Processes. Hence, it is potentially a promising tool to learn and control complex dynamical systems. In this letter, we develop a scalable abstraction-based framework that enables the use of DKL for control synthesis of stochastic dynamical systems against complex specifications. Specifically, we consider temporal logic specifications and create an end-to-end framework that uses DKL to learn an unknown system from data and formally abstracts the DKL model into an interval Markov decision process to perform control synthesis with correctness guarantees. Furthermore, we identify a deep architecture that enables accurate learning and efficient abstraction computation. The effectiveness of our approach is illustrated on various benchmarks, including a 5-D nonlinear stochastic system, showing how control synthesis with DKL can substantially outperform state-of-the-art competitive methods.