Strongly confined photonic modes can couple to quantum emitters and mechanical excitations. To harness the full potential in quantum photonic circuits, interactions between different constituents have to be precisely and dynamically controlled. Here, a prototypical coupled element, a photonic molecule defined in a photonic crystal membrane, is controlled by a radio frequency surface acoustic wave. The sound wave is tailored to deliberately switch on and off the bond of the photonic molecule on sub-nanosecond timescales. In time-resolved experiments, the acousto-optically controllable coupling is directly observed as clear anticrossings between the two nanophotonic modes. The coupling strength is determined directly from the experimental data. Both the time dependence of the tuning and the inter-cavity coupling strength are found to be in excellent agreement with numerical calculations. The demonstrated mechanical technique can be directly applied for dynamic quantum gate operations in state-of-the-art-coupled nanophotonic, quantum cavity electrodynamic and optomechanical systems.