A machine control system for use with a machine having a power source and a transmission is disclosed. The machine control system may have a clutch configured to connect an output of the power source with an input of the transmission. The machine control system may also have a sensor configured to generate a signal indicative of a speed of the power source, and a controller in communication with the clutch and the sensor. The controller may be configured to vary an actuating force of the clutch based on the signal.