A replay looked to be on the cards in an uninspiring encounter between the Championship rivals, with Burnley seeming content to settle for a draw after Brian Stock was sent off for two bookable offences in the first half.
Barnsley wasted several chances to take the lead and it looked like they would be unable to make their man advantage count until Rose, who had only been on the pitch a matter of seconds, converted after Brian Jensen had made a hash of David Perkins' free-kick.
Wales international Craig Davies was omitted from the squad amid reports Barnsley had accepted a £300,000 bid from Championship rivals Bolton, with Marlon Harewood stepping into the breach.
There was little on show to keep the fans interested in the early stages, with Burnley striker Sam Vokes tamely shooting wide in plenty of space.
However, tempers flared when Stock and Harewood tangled in an off-the-ball incident which saw both players booked for their troubles.
And Burnley were reduced to 10 men when Stock earned a second yellow card eight minutes before the break for a late challenge on Jim O'Brien.
Unsurprisingly the dismissal seemed to galvanise Barnsley, who dominated up until the interval with Perkins' curling free-kick from distance only just missing the target.
Full-back Scott Golbourne then wasted the best chance of the half when he blazed over with just Burnley goalkeeper Jensen to beat following some good build-up play from Chris Dagnall.
After the interval, Stephen Dawson dragged his shot wide after O'Brien's cross into the area had fallen to him and the midfielder wasted another glorious opportunity by firing over following some patient build-up play on the left.
Their profligacy nearly came back to haunt them but Vokes struck narrowly wide from Ross Wallace's cutback while Jason Shackell headed harmlessly over the bar from Kieran Trippier's corner.
The Barnsley fans were starting to grow restless with their side's lack of endeavour but the opener came in bizarre fashion in the 85th minute.
Perkins' floated free-kick should have presented no danger but Jensen could only tip the ball onto the bar, with substitute Rose, who had only just entered the fray, on hand to bundle home.