The 21-year-old joined the League Two side at the start of the season on an initial one-month deal.
However, he will now remain at Victoria Park until the end of November following a fresh agreement between the clubs.
"We're pleased to get things done with Scott because he's a good defender who has done well since he came here," manager Colin Cooper told Hartlepool's official website.
"He was keen to stay with us after his first month expired because he's really enjoying his football so we're delighted we've been able to get the deal finalised."
Harrison has made four appearances for Hartlepool so far this season.