O'Brien's effort gave the Tykes a fifth-minute lead, and the home side looked bereft of ideas in the opening period. They improved after the break and fought back through Mustapha Carayol and Curtis Main.
However, having gone in front Boro were punished for resting on their laurels as Scott Golbourne bundled home after Jason Steele failed to deal with Rory Delap's long throw, before Scotland sealed the hosts' fate from an indirect free-kick after the Boro goalkeeper picked up Rhys Williams' back-pass on the edge of his six-yard box.
"Managers at the bottom end of the table normally come in and complain about things going against them - deflected goals and a bit of bad luck - I feel a bit like that at the moment," said Mowbray, whose side remain in the play-off places despite another defeat.
"It was a kick in the teeth after five minutes with the huge deflected goal.
"We've found it hard work first half, a frustrating 45 minutes, but did well to get back in front so to lose it from that point is very, very disappointing.
"I can't question their commitment to win the game; I can feel their frustration in the dressing room at the end. We've given everything we can to try and change it around.
"How do you get out of it? You stick together, you work hard, and you try to do the right things every day. You have to keep going."
- Sports & Recreation
- Scott Golbourne
- Mustapha Carayol