A control system for use with an excavation machine is disclosed. The control system may have a boom member, a linear actuator connected to pivot the boom member in a first direction, a rotary actuator connected to swing the boom member in a second direction substantially orthogonal to the first direction, and an operator input device configured to generate a command signal indicative of a desired movement of the boom member. The control system may also have a tilt sensor configured to detect an inclination of the excavation machine, and a controller in communication with the rotary actuator, the operator input device, and the tilt sensor. The controller may be configured to receive a swing end stop for the boom member, to control the rotary actuator to move the boom member based on the command signal, and to modify the command signal to inhibit movement of the boom member past the swing end stop based on the detected inclination of the excavation machine.