Pools completed a double over Martin Scott's Middlesbrough Reserve side after a comfortable 2-0 victory at Billingham Synthonia.
Second half goals from David Foley and Billy Greulich did the damage for Colin West's men, who also defeated Leeds United last time out.
A tame first half was one of few chances; Michael Mackay had the best of the openings; Alan Power twice providing half chances for the striker but he sent the first snapshot across goal while his diving header from Power's cross also went wide.
At the other end, the best that Boro could muster was an effort straight at Mark Cook from James Cronesbury, while Marvin Emnes drove a shot just too high from distance.
Middlesbrough started the second half looking in more determined mood but Ashley Corker's effort was deflected off a defender and hit the post before going wide.
Pools rallied and were soon in front when Jon-Andre Fredriksen's shot was half blocked, only for Foley to nip in and round the keeper to fire home from close range.
Mackay had a chance to double the lead when Pools hit Boro on the counter with a long clearance from Cook, but the striker fired his volley too close to the keeper Adam Smith who held the shot.
With twenty minutes remaining, the hosts were given a boost when Ben Clark was shown a straight red card for getting involved with Kieran Edwards after a meaty challenge between the pair.
Armann Bjornsson dropped in to the centre-back role alongside Julian Cherel and the pair helped keep Boro at arms length for the remainder of the game.
And just when it looked like Boro were running out of ideas, Pools countered to win a left-wing corner which was slung over by Jonny Rowell for substitute Greulich to glance home with his head and seal the victory.
Full Time: Middlesbrough 0 Pools 2
Middlesbrough: Smith, Shead, Corker, K Edwards, Oliver, Weldon, Cronseberry, Dolan, Martin, Park (Brobbel 68), Emnes.
Subs not used: Ripley, Wyke, Hawkins, C Edwards.
Pools: Cook, McSweeney, Cherel, Clark, Haslam, Foley, Rowell, Power, Fredriksen, Mackay (Greulich 82), Bjornsson.
Subs not used: Tymon, Liddle, Purvis, Herbert.
