Complex dynamical systems, such as particle accelerators, often require complicated and time-consuming tuning procedures for optimal performance. It may also be required that these procedures estimate the optimal system parameters, which govern the dynamics of a spatiotemporal beam -- this can be a high-dimensional optimization problem. To address this, we propose a Classifier-pruned Bayesian Optimization-based Latent space Tuner (CBOL-Tuner), a framework for efficient exploration within a temporally-structured latent space. The CBOL-Tuner integrates a convolutional variational autoencoder (CVAE) for latent space representation, a long short-term memory (LSTM) network for temporal dynamics, a dense neural network (DNN) for parameter estimation, and a classifier-pruned Bayesian optimizer (C-BO) to adaptively search and filter the latent space for optimal solutions. CBOL-Tuner demonstrates superior performance in identifying multiple optimal settings and outperforms alternative global optimization methods.