Gary Liddle played in April's 2-0 victory over Brighton when he should have been serving a suspension for picking up 10 bookings, earning the club a three-point deduction.
The FA have also handed an extra one-match ban to the player, which will begin in 14 days, while fining the club £3,500.
A Football Disciplinary Commission decided to impose a points deduction and a suspended fine of £10,000 on the club, meaning they are now just a point clear of the bottom four going into the final weekend of the season.
The club have 28 days to lodge an appeal to the Football League and are considering their position.
Victory would secure survival but Pools would also be safe if Exeter and Tranmere fail to win.
Director of sport Chris Turner will pick from an unchanged squad, with Denis Behan pushing for a start after coming off the bench to net the leveller in last weekend's 1-1 draw with Exeter.