Scowen netted a couple of minutes into the second half at Loftus Road, where Rangers played the final 19 minutes with 10 men after Ryan Manning was sent off for a challenge on Matt Mills shortly after coming on as a substitute.
Scowen's goal was his first since joining Rangers from Barnsley last summer.
The midfielder collected the ball 25 yards out and bent a glorious shot beyond goalkeeper Nick Townsend and into the far corner of the net.
Relegation-threatened Barnsley, whose head coach Paul Heckingbottom signed a new contract this week, have won just one of their last 15 league games.
And they have now lost on 11 consecutive visits to QPR, where the Tykes have not won since 1950.
But they were the better side for much of the first half and would have gone ahead just before the interval had keeper Alex Smithies not produced a brilliant save to claw away Adam Hammill's right-footed effort.
Smithies had earlier gathered a low shot from George Moncur before Mills, on his Barnsley debut, hooked the ball over from close range after the home side struggled to deal with Hammill's free-kick.
Smithies was called into action again when Kieffer Moore sent a weak shot straight at him after being set up by Moncur.
Rangers' best moments of the first half came when Joel Lynch's left-wing cross just evaded Pawel Wszolek at the far post and when Luke Freeman's corner was headed over by James Perch, who played for the first time since suffering a broken kneecap in August.
Scowen's decisive strike soon after the restart settled the hosts, and took the wind out of their visitors' sails.
Having looked lively before going behind, Barnsley ran out of ideas and struggled to create chances even after Manning's red card.
Tom Bradshaw had a decent opportunity but fired straight at Smithies and Lynch prevented a late equaliser by blocking Moncur's goal-bound shot.
At the other end, Conor Washington twice failed to find a way past Townsend, first after Perch had headed down Freeman's free-kick and then when the striker was through on goal following Jack Robinson's throw-in.
Townsend produced a similar stop in stoppage time when he saved at the feet of QPR substitute Bright Osayi-Samuel.
Tykes boss Paul Heckingbottom said: “We needed to score when we were on top in the first half, we had some really good opportunities and should have capitalised on that.
“You’ve got take them. That’s been our season, not scoring whilst you’re on top is a big thing. B
“ecause of how competitive this league is you know that the opposition will have a moment in the game as well, and today they have taken theirs.”