This paper presents the application of a perturbation method for the closed-loop dynamic simulation of a rigid-link manipulator with joint friction. In this method the perturbed motion of the manipulator is modelled as a first-order perturbation of the nominal manipulator motion. A non-linear finite element method is used to formulate the dynamic equations of the manipulator mechanism. In a closed-loop simulation the driving torques are generated by the control system. Friction torques at the actuator joints are introduced at the stage of perturbed dynamics. For a mathematical model of the friction torques we implemented the LuGre friction model that accounts both for the sliding and presliding regime. To illustrate the method, the motion of a six-axes industrial St¨aubli robot is simulated. The manipulation task implies transferring a laser spot along a straight line with a trapezoidal velocity profile. The computed trajectory tracking errors are compared with measured values, where in both cases the tip position is computed from the joint angles using a nominal kinematic robot model. It is found that a closed-loop simulation using a non-linear finite element model of this robot is very time-consuming due to the small time step of the discrete controller. Using the perturbation method with the linearised model a substantial reduction of the computer time is achieved without loss of accuracy.