Rhynchocephalia and Squamata diverged in the Triassic, more than 200 million years ago. Rhynchocephalians were diverse through the Mesozoic; today the order has one living genus, confined to New Zealand. Calling a tuatara a lizard is about as accurate as calling a crocodile a lizard.
The anatomy carries the difference. Tuatara have two complete temporal openings in the skull, an arrangement lizards have modified. The teeth are fused to the jaw bones rather than socketed or attached to the inner face, and are not replaced; a single row in the lower jaw shears between two rows in the upper. They have no external ear opening and no copulatory organ, so mating is by cloacal apposition. They remain active at body temperatures around 11 to 13 degrees Celsius, low for a reptile.
The pineal or parietal eye on top of the head, with lens, retina and nerve, is often called unique. It is not: many lizards have one. In tuatara it is unusually well developed in juveniles and becomes covered by scales with age. Its function is thought to involve seasonal and daily timing rather than image formation.