A control system for a machine is disclosed. The control system may have a first sensor configured to generate a first signal indicative of an inclination of the machine, a second sensor configured to generate a second signal indicative of a travel speed of the machine, a third sensor configured to generate a third signal indicative of an engine speed of the machine, and a controller disposed in communication with each of the first, second, and third sensors. The controller is configured to determine whether the machine is freewheeling in a neutral gear, and to generate a machine braking command based on at least one of the first, second, and third signals. A method of retarding a machine is also disclosed.