Middlesbrough boss Gordon Strachan accepted his side failed to cope with Barnsley's second-half revival.
Justin Hoyte gave Boro a half-time lead but goals from Steve Foster and Hugo Colace earned the Tykes the points.
Strachan said: "We won the football match in the first half and they decided to turn it into a cup tie and then they won it. We were disappointed to lose the game but we couldn't match them in a different game."
Copyright (c) PA Sport 2009, All Rights Reserved.
Do YOU want to write for GiveMeSport? Get started today by signing-up and submitting an article HERE: https://www.givemesport.com/writeforgms