The Clarets’ hopes of advancing in the Premier League Cup suffered a major blow with a second successive defeat in Group G.
Burnley will now have to win their final two games – away at Crystal Palace and group leaders Blackburn Rovers – to have any chance of securing a top-two finish and progress to the knock-out stages.
And with many of their more senior players out on loan that looks a demanding task.
The Clarets had five scholars in their starting line-up against a Boro side which scored either side of the break through Tyrone O’Neill and then survived a late Ali Koiki penalty to tighten their grip on second place with a second group win.