Boro went down to a first half double from Huddersfield as progression in the Premier League Cup lies firmly in the balance with two games to spare.
Goals from Kian Harratt and Charles Ondo did the damage to the Teessiders but with Watford beating West Brom, the Reds still sit in the second qualification spot.
Boro had the first effort on target in the game after 18 minutes when Afonso Lindo powered a header straight at the Town keeper.
From then on the Terriers took hold of the game, first when Kian Harratt swivelled and fired in at the near post before Charles Ondo rifled home in the far corner from the edge of the box to make it two.
Boro came close to pulling one back on the stroke of half time following a good interchange between Fenton John and Calum Kavanagh down the left. The latter floated in a cross which Bilokapic spilled on to Jeremy Sivi’s head. The ball looked to be rolling in before a late Town clearance kept them two goals ahead at the break.
Bryant Bilongo came close with a header from a corner shortly after half time before Kavanagh forced a smart stop out of Bilokapic low down to his left hand side following a good run from Fenton.
Max Metcalfe had to be alert to stop Harratt getting his second with a reaction save down to his right seconds later.
Boro now face the other two sides vying to qualify, with West Brom first on the agenda.