This follows a forensic investigation by Treasury into the procurement of the IEC’s Riverside Office Park building in Centurion, Pretoria.
The probe found the process was neither fair, transparent, nor cost-effective.
It found Tlakula did not give guidance or formally inform various people what was expected of them in the process.
The Treasury’s report followed a recommendation by Public Protector Thuli Madonsela in her own report into the matter, released in August last year.
She said the process of trying to clear her name had been long drawn out and for the sake of the institution, she decided to abandon this process and resign.
Terry Tselane, Deputy IEC Chairperson says this would give back the credibility the institution deserves and will allow them the process to start preparing for the 2015 Municipal Elections without any dark clouds hovering over them.
Various political parties also agreed with her resignation.