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The 24-year-old from Glendale, Arizona, was named in the bottom three along with Kristy Lee Cook and Syesha Mercado.
After host Ryan Seacrest revealed the results of the 29 million votes, Hernandez said: "Honestly, things happen for a reason."
Visibly shocked, Hernandez added: "I think we all have a plan. This isn't it for me."
This week, the Idol contestants performed Beatles tracks with Hernandez singing 'I Saw Her Standing There'.
Stand out performances came from Carly Smithson (who sang 'Come Together'), Brooke White ('Let It Be'), David Cook ('Eleanor Rigby') and Chikezie ('She's a Woman').
David Archuleta, the competition favourite, forgot the words to 'We Can Work It Out' three times during the song.
Hernandez was recently involved in a sex scandal when it was revealed he used to work as a stripper.
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