A control system for a power unit having a supply of fuel and a supply of reductant is disclosed. The control system may have a first sensor associated with the supply of fuel to generate a signal indicative of a quantity of fuel remaining. The control system may also have a second sensor associated with the supply of reductant to generate a signal indicative of a quantity of the reductant remaining. The control system may further have a controller in communication with the first and second sensors. The controller may be configured to affect operation of the power unit such that the remaining fuel is consumed before consumption of the remaining reductant.