Smith was suspended for one test, voluntarily stood down for another and received an official warning from New Zealand Rugby last year following revelations of the liaison.
Australian media in August published what they said were messages between the woman and Smith which they said proved he had misled All Blacks management about the nature of their relationship.
NZR said in a news release on Saturday that the second probe had revealed "some inconsistencies" between Smith's testimony and the information published in the media, but it had not had a "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 NZR," said NZR chief Steve Tew.
"To reinforce this point, we have issued Aaron Smith with a formal written warning."
(Writing by Nick Mulvenney in Sydney, Editing by Gene Cherry)
