Goals from Luke Molyneux and David Ferguson either side of half time saw Hartlepool come from behind to claim all three points at The EnviroVent Stadium.
Luke Armstrong had put Town ahead after 21 minutes, though that lead lasted just four minutes, with Town not being able to find an equaliser after Ferguson's 61st minute finish.
Simon Weaver made two changes from Tuesday night as Ryan Fallowfield and Lewis Richards replaced Josh Falkingham and Nathan Sheron, while Simon Power returned to the bench after a long spell on the sidelines.
Town showed their intentions within the first 30 seconds, the ball being played quickly up to the front three resulting in Jack Diamond stinging the arms of Ben Killip.
Armstrong put Town ahead in the 21st minute, collecting Jack Muldoon's pass before shifting the ball onto his left foot and slotting home against his former team.
Pools were level just four minutes later though as Molyneux scored a goal of real quality, the winger cutting inside on his left foot and finding the top corner from 25 yards out.
The visitors went close to taking the lead ten minutes before the break when Omar Bogle's hold up play set up Tom Crawford who placed his shot the wrong side of the post.
After the restart, Mark Oxley was needed to prevent Hartlepool taking the lead, Town's stopper keeping out Bogle's effort with a one handed save after David Ferguson had carried the ball forward and found his teammate.
The chances kept falling the way of the visitors with Joe Grey somehow not converting at the back post, before seeing his header tipped over the bar by Oxley.
A second Hartlepool goal had been coming and arrived in the 61st minute when Bogle's pass to the edge of the area was dispatched first time into to the bottom corner by the left foot of Ferguson.
Calum Kavanagh was introduced in the 65th minute and should have put his side on level terms ten minutes after his arrival, getting on the end of Lewis Page's low cross at the near post but being unable to guide the ball below the bar.
Diamond went close next, but saw his left footed drive beaten away by Killip before substitutes Simon Power and Kavanagh combined, though the latter couldn't hit the target with his back post header, meaning Pools departed with all three points.
Town: Oxley, Fallowfield (Beck 91), Page, Smith, Burrell, Thomson, Pattison, Muldoon (Kavanagh 65), Diamond, Armstrong, Richards (Power 76)
Subs not used: Cracknell, Sheron, Austerfield
Goals: Armstrong 21
Hartlepool: Killip, Sterry, Ferguson, Liddle, Odusina, Shelton, Bogle (Carver 86), Featherstone, Molyneux (Hull 92), Grey (White 76), Crawford
Subs not used: Holohan, Smith, Fletcher, Bilokapic
Goals: Molyneux 25, Ferguson 61
Referee: C Boyeson
Attendance: 2,368 (597 away)