Defences were on top during a cagey first half and it was the tricky Luke Freeman who had the first shot on target when he wriggled in to space and fired on goal but Scott Flinders was well behind it.
The dangerous Lucas Akins skipped in to space down the right and whipped a well-placed cross in to the box only for front man Dani Lopez to produce an air shot and Pools were able to clear.
Darren Holden was in the starting eleven for the injured Evan Horwood and almost marked his return to the action with a stunning goal but, after driving forward and cutting inside, he curled a right-footed effort just too high.
Pools ended the half well and Sam Collins could have become an unlikely scorer when a corner fell to him on the edge of the box but his volley through a crowded area was deflected just wide.
And they carried their momentum over in to the start of the second period when Neil Austin curled a free-kick on target which was held by home keeper Steve Arnold.
At the other end Stevenage came as close to scoring as either team had all afternoon when a left-wing corner was helped on at the front post but it looped agonisingly beyond the back post, and the chasing home duo of Marcus Haber and Mark Roberts.
A clever Charlie Wyke flick set Jonathan Franks away down the right flank and he drove at the hosts' defence before cutting in on his left foot but in the end sent his shot high over the bar.
Akins volleyed wide after Flinders had punched clear an inswinging corner, while Freeman dragged a shot wide of the front post from the edge of the area following a rare slip from Peter Hartley had allowed substitute Filipe Morais to create the chance.
Hughes introduced Luke James to the action and the youngster almost made an immediate impact when he scampered after Wyke's through ball but he drilled his shot just wide of the far post with Arnold seemingly beaten.
Holden then darted forward in to space and showed a clean pair of heels to Akins as he made for the byline from where he pulled it back to James who swivelled and got a shot off only to see it blocked away to safety.
Pools were building up a head of steam and were looking the most likely to open the scoring - and then, with fifteen minutes remaining, they were hit by a Stevenage sucker punch.
Freeman evaded two or three tackles as he made his way infield from the left and then flicked it square for Morais; the striker got a shot away which was blocked but it spun out towards the left of the box where full-back Max Ehmer gleefully ran on to it and smashed it low past Flinders.
It was a bitter pill to swallow and the disappointment seemed to deflate Pools for a couple of minutes as James Dunne skilfully skipped away down the right to cross for Freeman who looked odds on to double the lead only to be brilliantly denied by Flinders.
Even still, after that Pools toiled to try and get back on level terms but despite getting the ball in to the hosts' penalty area at regular intervals it wouldn't drop kindly and the home side clung to the points.
Full Time: Stevenage 1 Pools 0
Booked: Baldwin (26), Monkhouse (63)
Pools: Flinders, Austin, Collins, Hartley, Holden, Walton, Humphreys, Baldwin (James 66), Monkhouse, Franks (Rutherford 87), Wyke.
Subs Not Used: McHugh, Buddle, Rowbotham, Hawkins, Boagey.
Stevenage: Arnold, Gray, Roberts, Ngala, Dunne, Shroot (Grant 23), Ehmer, Haber, Akins (Deacon 80), Freeman, Lopez (Morais 59).
Subs Not Used: Day, Smith, Jeffrey, Hoskins.