Santiago, who was among the last six finalists on the Fox show, was the first of two acts to be eliminated based on public votes during the program's December 5 episode.
The announcement of the 17-year-old singer's elimination was met with boos from the audience. Her mentor, judge Demi Lovato, was heard saying, "This is ridiculous!"
Judge Kelly Rowland also appeared shocked at the announcement.
"This is a real shock here on the stage and in the audience," host Mario Lopez said as he called on both Santiago and Lovato to take center stage.
Asked for her thoughts on being sent home, Santiago said, "A lot's going through my mind and... I don't know, I guess I didn't give the strongest performance last night, and I just hope I can have another change again, but..."
"I'm actually pretty speechless and disappointed," said Lovato, who was standing beside Santiago. "I feel like a lot of really amazing people have been sent home that didn't deserve to go home so soon, and Ellona is definitely one of them."
"She could have won this competition," Lovato added.
Stellar run
Santiago, who became known in the competition for her "diva" performances, was seen as one of the frontrunners on "The X Factor USA" after consecutive raves from judges until reaching the top 6.
The Pinay's last numbers on the show were "unplugged" renditions of Lady Gaga's "Applause" and Beyonce's "If I Were a Boy," which garnered glowing reviews from the judges.
Paulina Rubio called her a "superstar," with fellow judge Simon Cowell referring to one of her numbers as "incredible." Addressing her mentee, Lovato also said, "America should vote for you because you deserve it!"
Santiago, however, went on to garner the fewest votes.
Fellow finalists Rion Paige, who was also mentored by Lovato, and Carlito Olivero were also in the bottom three in terms of public votes. The two acts sang "for survival," with Olivero moving on based on his last-chance performance.
He joins duo Alex & Sierra, Jeff Gutt, and band Restless Road in the semifinals of "The X Factor USA," which will kick off next week.
'Best is yet to come'
"Just because I'm off the show doesn't mean my dream ends, keep a lookout for me," she asid. "Thank you so much for all the people who voted me each week and kept me this far, and thank you even though many of you couldn't but continuously supported me along the way."
"I'm blessed, grateful, and the best is yet to come. I love you all!"
In an earlier interview with ABS-CBN News, Santiago said she was hoping to win the competition to give her parents a better life. She said she wants to repay them for their sacrifices for her and her siblings.
Born in the Philippines, Santiago's family moved to San Lorenzo, California when she was only 11 months old.
Ellona, eliminated in X Factor USA Season 3
Ellona's exit interview
