Pools defended firmly and in numbers - and rode their luck at times – but were ready to return home with a 0-0 draw.
But in the 90th minute, substitute Koby Arthur leapt inside the penalty area to head in from around eight yards.
The Robins twice hit the frame of the goal, first through Matt Richards in the first half, then substitute John Marquis after his second-half appearance.
Scott Flinders made a wonder save on 83 minutes, tipping a goalbound Marquis header onto the underside of the bar.
Pools didn’t create a lot at the other end, but the efforts of strikers Charlie Wyke and Marlon Harewood – scorers last time out at Wimbledon – couldn’t be faulted.
CHELTENHAM TOWN (3-5-2): Carson; M Taylor, Brown, Elliott; Vaughan (Sterling-James 71), Wynter, Richards, J Taylor, Braham-Barrett; Harrison (Arthur 77), Gornell (Marquis 60). Subs: Haworth, Deaman, Hanks, Black.
HARTLEPOOL UNITED: Flinders; Duckworth, Bates, Collins, Austin; Franks (James 90), Miller, Walker, Brobbel (Compton 90); Wyke, Harewood (Woods 70). Subs: Holden, Richards, Harrison, Dixon (gk).