In this paper, the optimized Fuzzy Logic controlled three-phase Shunt Active Power Filters (SAPF) to eliminate harmonics of line current, correct power factor, balanced and unbalanced loads are given. To efficiently operate the system, Ant Colony Algorithm (ACA) optimizes this fuzzy logic controller. The controller is customized by adding a tuning controller to improve filter performance for lighter loads, in- addition, this tuning controller controls the output parameter of Shunt Active Power Filter (SAPF) by tuned to an optimized value. This optimized SAPF system has very short response time delay for different complex power quality issues and various compensation purposes. The system obtains dissimilar compensating current references accurately and easily. Moreover, Simulation shows that installation of this optimized controller in the SAPF system eliminates harmonics and corrects the waveform of the line current and corrected power factor. Simulation results obtained with MATLAB and testing results on a shunt APF are presented to validate the performance of the compensation system.