A fabrication system is disclosed for use in joining two components of a work piece. The fabrication system may have a mount configured to hold the work piece with a void to be filled with material. The fabrication system may also have a scanner configured to capture at least one image of the void, a robotic fabrication device movable relative to the mount, and a controller in communication with the scanner and the robotic fabrication device. The controller may be configured to generate a model of the void based on the at least one image, and to slice the model into at least one layer. The controller may also be configured to develop a tool path for each of the at least one layer, and to cause the robotic fabrication device to deposit material within the void based on the tool path.