The Reds made it much harder work than it should have been but all that matters is that Flitcroft's men claimed three points after a performance, particularly first half, to be proud of.
Middlesbrough must be given credit for coming back at the Reds but the first half gave them too steep of a hill to climb.
Both sets of fans were in good voice at the off but they had to wait a while to see either side have an effort on goal.
The first real chance of the game didn't come until the 18th minutes, and it was Chris O'Grady who created the chance for himself. With his back to goal he turned his man and got to the byline before Steele blocked his shot and Boro cleared the rebound.
After the referee waved play on following Pedersen receiving a challenge from behind, Mellis worked the ball to McCourt on the right and he jinked towards the box before curling an audacious attempt towards the top corner with the outside of his right boot but it sailed wide on 21 minutes.
On 25 minutes the visitors really should have taken the lead as Lukas Jutkiewicz sprang clean through and only had Butland to beat but he blazed well over the bar with all the time in the world.
At the other end Paddy McCourt didn't blaze his chance as he opened up his Reds account with a great individual goal. Somehow Paddy worked his way through a crowd of Middlesbrough players before poking into the corner.
Unfortunately for Paddy, on 28 minutes he was brought off for Jim O'Brien after picking up a knock during his run.
A well-worked set-piece from Boro saw a header straight at Butland, and the visitors were made to pay as O'Brien's shot deflected off O'Grady and wrong-footed Steele. The Reds finally had some good fortune.
Marcus Pedersen burst into the box on 42 minutes and was brought down, which gave Chris O'Grady a chance from the spot. For his sixth goal of the season, he thundered into the top bag for 3-0.
It could have been four for the Reds as Mellis volleyed wide after initially sending the ball in for Pedersen.
Boro replaced former Red Jacob Butterfield with Marvin Emnes as they looked to claw their way back into the match. A header from Kamara was straight at Butland two minutes into the second half - the third headed attempt to find the hands of the England international.
Marcus Pedersen had a glorious chance to make it four when O'Brien sent him through on the counter - the Norwegian international attempted to chip Steele who was way off his line but he scuffed his 35 yard effort wide.
Mellis was replaced by Cywka out wide after a brilliant shift from the former Chelsea man, with 26 minutes left on the watch.
The Reds weren't being caused any serious problems at the back, and looked a threat on the break with O'Brien and Cywka on each flank.
Barnsley's third and final change came as Marcus Pedersen was replaced by Jason Scotland in attack on 75 minutes.
Nobody gave O'Brien a call for 'man on' which gave Carayol the chance to curl one at goal on 78 minutes but his effort from the left-hand side of the box clipped the bar on its way over.
Cywka's looping cross was greeted well by the leap of O'Brien in the area but his effort sailed wide with Steele scrambling away to his left.
At the other end Jack Butland proved his concentration levels were still sky-high as Emnes let rip from 25 yards, but Butland tipped the ball past the post with a brilliant fingertip save on 81 minutes.
Boro did pull one back with eight minutes left when Albert Adomah pulled a shot from the sky and it deflected beyond the despairing hand of Butland and looped in.
Two minutes later it was game on as Adomah nodded into the far corner to stun the Reds. From nowhere the Reds were now looking to hang on.
The momentum was with the visitors and a header from Friend deflected wide. Four minutes of stoppage time was indicated.
The final whistle brought relief to three sides of Oakwell as finally a performance that warranted three points, earned three points.
Reds: Butland, Kennedy, Cranie, Perkins, Wiseman, Pedersen (Scotland 75), Mellis (Cywka 64), M'voto, Fox, McCourt (O'Brien 27).
Subs: Hassell, Dawson, Jennings, Etuhu.
Middlesbrough: Steele, Whitehead, Richardson, Butterfield (Emnes 46), Kamara, Hines, Leadbitter, Jutkiewicz (Carayol 67), Gibson, Adomah, Friend.
Subs: Konstantopoulos, Williams, Parnaby, Varga, Smallwood.
Referee: Oliver Langford
Assistant Referees: Richard Bartlett & Christopher Kavanagh
Fourth Official: Ryan Johnson
Man of the match, sponsored by Napoleons: Chris O'Grady