Henderson became the latest act to be eliminated from the ITV show after falling into the bottom two with James Arthur.
The result of the viewers' vote was met with shock and disapproval from the studio audience and with huge surprise from the judges.
Both acts returned to the stage to perform in the sing-off against one another. Henderson performed a rendition of Daniel Bedingfield's 'If You're Not The One' before Arthur sung 'Fallin' by Alicia Keys.
Host Dermot O'Leary then turned to the judges for their votes. Henderson's mentor Tulisa Contostavlos expressed her anger at the "ridiculous" result, saying that viewers were voting for the "wrong people". She then chose to send home Arthur. Nicole Scherzinger, Arthur's mentor, chose to send home Henderson.
Louis Walsh commented on the fact that both acts had so much potential in the competition, before choosing to send home James Arthur. Gary Barlow chose to send home Henderson and took the decision to Deadlock.
It was then revealed that the 16-year-old had polled the fewest amount of votes from the public.
Henderson was visibly upset at her exit from the competition and was consoled by James Arthur following the announcement.
On The Xtra Factor, Contostavlos said she was "lost for words" after losing her final act in the competition. When asked if her act could have done any more this week to help her survive, she said she could not. She described Henderson's performance of 'You're The One That I Want' as "one of her best".
The 'Young' singer added that she will now be rooting for the acts she likes in the competition and pushing for them to go all the way to the final.
Henderson had been the favourite to win the ITV show throughout the series until earlier this week, when Jahmene Douglas became the bookies' favourite to triumph.
Both Henderson and Arthur had been widely tipped to make the final after consistently positive comments from the judges. James Arthur topped this week's Digital Spy poll for best singer on Saturday's (November 17) live show.
Watch Ella Henderson's performance of 'Believe' at Boot Camp earlier this year below:
The X Factor 2012 Results Show 7: