NZR launched a new independent investigation in August after the release of messages between Smith and the woman at the centre of the incident in Australian media, which contradicted his account of affairs during the original disciplinary hearing.
NZR said the investigator had concluded that, while there were inconsistencies between Smith's account at the time and the information released in the exchanges with the woman, it was determined this did not have any material impact on the outcome of the original hearing.
"Being honest, particularly in a disciplinary proceeding, is critically important for any employer and that is certainly the case with New Zealand Rugby," NZR chief executive Steve Tew said.
"To reinforce this point, we have issued Aaron Smith with a formal written warning."
Smith had sex with a woman in a disabled toilet at Christchurch Airport in September last year, and was seen by members of the public going into the toilet.
The Highlanders player returned home from South Africa to face the music, which was framed as a leadership group decision to suspend him for one match.
An internal investigation by NZR deemed this to be appropriate punishment and the saga would have ended there except in August the woman, who has not been named, released a tranche of messages between her and Smith that indicated he had sanitised his version of events and attempted to coerce her into making a false statement.
At that point, NZR ordered an independent investigation into the incident.
The dump of correspondence came at the most awkward time for NZR, which was preparing to release the findings of an independent Respect and Responsibility Review, commissioned in the wake of a bad year for off-field behaviour.
Among other things this review found that NZR needed to do a better job of educating players about the perils of excess alcohol intake and attitudes towards women.