Mr Cook said a forthcoming update to iOS would enable users to disable the feature, which reduces mobile performance as a device's battery ages in order to prevent it shutting down unexpectedly.
The emergence of the feature in December linked to the iPhone 6, 6 Plus, 6s, 6s Plus and SE led to an outcry from some users and questions from French and US authorities.
Now Mr Cook has told US network ABC that users would be given the option to turn off the feature, despite the company not recommending that customers do so.
"We're going to give people the visibility of the health of their battery, so it's very, very transparent. This hasn't been done before," he said.
"We will tell somebody we're slightly reducing your performance by some amount in order to not have an unexpected restart and if you don't want it, you can turn it off. Now we don't recommend it because we think people's iPhones are really important to them and you never can tell when something is so urgent."
The Apple chief executive also said the company could have been clearer on how the technology worked, having admitted last month that it used the feature to combat battery degradation.
The company apologised at the time and cut the price of replacement batteries, but denied it applied the slowdown as a means to encourage users to upgrade their phone.
"Our actions were all in service of the user, I can't stress that enough. Maybe we should have been clearer at a point in time but our actions were always the purest," he said.
"If anybody out there believes we did something nefariously, we apologise for any kind of thing we did or didn't do."
The company has been contacted by the US Senate over the practice, while authorities in France have opened an investigation into the issue under the country's "planned obsolescence" laws.