The Pirates of the Caribbean actor joined the singer's metal band on guitar for the tracks 'The Beautiful People' and 'Sweet Dreams (Are Made of This)'.
The band were performing at Revolver's Golden Gods 2012 Awards at Club Nokia in LA last night (April 11).
Many audience members were not aware of Depp's presence on stage, until Manson said: "If you don't recognise my personal friend... my personal saviour, my personal guitar hero, Johnny Depp!"
The 48-year-old actor will appear on drums and lead guitar for a cover of Carly Simon's 'You're So Vain' on Manson's eighth studio album Born Villain.
Johnny Depp will next be seen in Tim Burton's Dark Shadows, which is out at cinemas on May 11.
Born Villain is set to be released on April 30.
> Marilyn Manson debuts 'No Reflection' music video
Watch the trailer for Dark Shadows below: