Beale was fined A$45,000 ($40,000) but escaped further punishment after a tribunal heard charges that he had sent 'deeply offensive' text messages about Wallabies' business manager, Di Patston, who resigned under stress amid the scandal.
Although omitted from Cheika's 33-man squad, announced upon his appointment on Wednesday, Beale walked away from Friday's code of conduct hearing with his national contract intact and free to join the tour for matches against Wales, France, Ireland and England, if called.
"The Australian Rugby Union today confirmed... Wallabies head coach Michael Cheika has advised Kurtley Beale will not join the squad for the Spring Tour," the ARU said in an emailed statement.
"From time to time there are changes to personnel during tours, due to injury or other matters, and we will advise if there are any changes to this position."
The squad flew out on Friday prior to Beale's hearing and Cheika was informed of the outcome while in transit, an ARU spokesperson said.
The decision was the coach's alone, the spokesperson added.
The 'text-gate' scandal was triggered by a seemingly innocuous in-flight row between Beale and Patston when the Wallabies were in transit to Argentina but quickly grew toxic after the ARU stood Beale down pending the independent hearing.
Amid heavy innuendo and media reports questioning the players' support, former test prop McKenzie sensationally quit hours before the 28-27 loss to the All Blacks last week and in the wake of Patston's own resignation.
Under Cheika, Beale played a key role in the Waratahs' maiden Super Rugby title, returning to career-best form after discipline and alcohol problems blighted his previous season at the Melbourne Rebels.
That the 47-test back is still eligible to play for Australia despite his poor off-field record has polarised opinions and ARU chief Bill Pulver is under fire for his handling of the case.
"His handling of the biggest public relations crisis in rugby's recent history, which saw Pulver blame the media for everything, has raised questions about his leadership," rugby writer Rebecca Wilson wrote in Saturday's Daily Telegraph, a Sydney newspaper.
Pulver was on the front foot against Beale, publicising detailed allegations against him and insisting on the hearing despite leaked text messages to the media that showed Beale and Patston had dealt privately with the matter months before their bust-up on a plane.
(Editing by Sudipto Ganguly)
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