We investigate vortex shedding from a moving penetrable obstacle in a highly oblate Bose-Einstein condensate. The penetrable obstacle is formed by a repulsive Gaussian laser beam that has the potential barrier height lower than the chemical potential of the condensate. The moving obstacle periodically generates vortex dipoles and the vortex shedding frequency f(upsilon) linearly increases with the obstacle velocity upsilon as f(upsilon) = a(upsilon -upsilon(c)), where upsilon(c) is a critical velocity. Based on the periodic shedding behavior, we demonstrate deterministic generation of a single vortex dipole by applying a short linear sweep of a laser beam. This method will allow further controlled vortex experiments such as dipole-dipole collisions.