The people who create a system have some intent for it. The system may or may not effectively achieve that intent, may or may not outlive the initial conditions that surrounded its creation, and may or may not have side effects.
Purpose is something humans assign. It is sometimes linked to intent. A carpenter's hammer is intended to drive and pull nails, and that is often also its purpose. The purpose of the hammer I keep in my basement is breaking open walnuts.
The phrase is stating that the purpose we should assign to systems when judging them is their outcome, and not the intent behind them.
The classic example is a hospital for treating cancer patients. Suppose that one third of the patients are successfully treated, while the other two thirds die of their cancer. Is the purpose of the hospital to kill two thirds of the patients? Clearly not, but that is the outcome.