"I...... was...... and just woke up," she wrote back. "I am … sorry … that my bags … offend u."
Hadid's fans leapt to her defence, saying the supermodel looked like a "real human" and "authentic".
"It's OK to have eye bags, you're human," one person wrote.
The original commenter also responded, expressing shock that Hadid had replied to her and praising her looks.
"You are so gorgeous! Your eye bags are a work of art," they wrote.
Earlier this week, the supermodel shared a video on Instagram revealing how she had become sunburnt after falling asleep outside.
"I just woke up. Danger do not leave a sleepy girl in the sun," she captioned the short clip.
Wearing the same blue bikini, Bella sported a painful burn across her chest and her face was red.
One concerned fan wrote: "Were u at least wearing sunscreen??"
"Wear sunscreen please bb," another added.
But others didn't even seem to notice the sunburn and were instead blown away by Hadid's incredible figure, commenting that she was "body goals".
Her supermodel sister Gigi appeared to be absent from the tropical getaway, with the new mum keeping a low profile since welcoming daughter Khai last year.
In an interview, Hadid revealed how older sister Gigi, 25, has made the decision to keep her little one's face off social media.
"I think she wants to be real online," Hadid told Vogue.
"But until her child wants to be in the spotlight and can make the decision herself, she doesn't want to put her in that position."
