An excavation control system for a machine is disclosed. The excavation control system may have a tool, at least one operator input device configured to provide manual control over movement of the tool, and a controller in communication with the at least one operator input device. The controller may be configured to receive an input related to an operator desired tool location, and determine that an operator is manually controlling movement of the tool toward the operator desired tool location. The controller may be further configured to automatically assume control over movement of the tool toward the operator desired tool location based on the determination.