The implementation of image-based phenotyping systems has become an important aspect of crop and plant science research which has shown tremendous growth over the years. Accurate determination of features using images requires stable imaging and very precise processing. By installing a camera on a mechanical arm driven by motor, the maintenance of accuracy and stability becomes non-trivial. As per the state-of-the-art, the issue of external camera shake incurred due to vibration is a great concern in capturing accurate images, which may be induced by the driving motor of the manipulator. So, there is a requirement for a stable active controller for sufficient vibration attenuation of the manipulator. However, there are very few reports in agricultural practices which use control algorithms. Although, many control strategies have been utilized to control the vibration in manipulators associated to various applications, no control strategy with validated stability has been provided to control the vibration in such envisioned agricultural manipulator with simple low-cost hardware devices with the compensation of non-linearities. So, in this work, the combination of proportional-integral-differential (PID) control with type-2 fuzzy logic (T2-F-PID) is implemented for vibration control. The validation of the controller stability using Lyapunov analysis is established. A torsional actuator (TA) is applied for mitigating torsional vibration, which is a new contribution in the area of agricultural manipulators. Also, to prove the effectiveness of the controller, the vibration attenuation results with T2-F-PID is compared with conventional PD/PID controllers, and a type-1 fuzzy PID (T1-F-PID) controller.