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In terms of humanoid (and not robotic) companions, the only known on-screen example was Clara Oswald, who was technically naked for part of "The Time of the Doctor" though we (the viewers) and some (not all) characters in the episode saw her with holographic clothing (for a time the Doctor also has holographic clothing, making the only on-screen occasion where a Doctor and his companion have been technically naked together on screen). River Song, being the Doctor's wife was implied to have had sex with the Doctor at some point (references in "The Impossible Astronaut", et al) so presumably the Doctor saw her naked at some point but where, when and, frankly, if has never been indicated on screen.

Other occasions may have taken place in audio or literary spin-offs.