Referee did not fully understand accepted paper

As is the custom on this site (or at least it should be) let's assume the premises of the question are correct - that is that it is indeed a prestigious journal.

Do nothing.

In fact no: celebrate acceptance in the way you find most appropriate.

The fact that some people misunderstand what you're trying to say is not a basis to act after acceptance. It might indicate that you presented your results in a not so clear manner — which would speak in favor of refining your writing for future articles — but that would not be an exception in the scientific literature. At any rate, edits (other than very minor ones such as typos) after final acceptance are generally not allowed.

If you see errors in your article that are not trivial and you feel need addressing, the appropriate way to handle this is to publish an erratum. I imagine most journals have a standard procedure for that.

Celebrate the acceptance, but rework the sections that were apparently poorly understood.

You will want your readers to fully understand and appreciate your contribution. A clear paper is not only more useful, it is also more frequently cited. If a reviewer, who more closely looks at your paper than the usual casual reader, misunderstands, this is a warning-signal.

In practical terms: You could approach the reviewer (via the editor, to be sure) with your concern that parts of the paper were not as clear as they could have been and politely ask whether she might explicate which passages could be improved in terms of their transparency. You could also ask other colleagues to have a look at your paper, focusing on the clarity of your writing. Also signal to the editor that you would like to make some minor stylistic revisions before submitting the final manuscript, so the editor knows what to expect and when.

It often happens that referees have no time to understand the papers they are supposed to review. It's a systematic consequence of the imperfection of the current peer-review‒system. At the moment, not so much could be done about it. Said that,

• there is no reason for celebration, since you are not sure whether your paper was intelligible,
• there is a reason to feel satisfied since the paper was accepted,
• but actions as you mentioned are neither required nor expected.

If you really wish to do something, you can improve the text at the earliest point the reviewer had a problem with. Of course, you could ask the editor to issue a request to the referee to tell you this earliest point, but the editor or referee may choose not to answer: it goes beyond the usual duties of their roles.

Too many improvements could be regarded as deviating too much from the accepted part. Typically, improvements are regarded as acceptable only if they address the concerns raised by the reviewers.