Conor Chaplin gave the Tykes the lead with a 58th minute header and Jacob Brown doubled the hosts advantage on 76 minutes after Rovers were reduced to ten men following Ben Brereton's red card.
The win lifts Barnsley off of the foot of the table and brings them within one point of safety, having gone unbeaten since the restart of the season with two wins and a draw.
Blackburn remain 10th after a second consecutive shutout loss and they trail sixth-place Cardiff City by five points for the final promotion play-off spot.
Story of the match
Barnsley manager Gerhard Struber made just one change to the side that drew 0-0 at Millwall, starting Jordan Williams at right wing back in place of Kilian Ludewig while Blackburn manager Tony Mowbray brought Charlie Mulgrew, Bradley Johnson, Dominic Samuel and Adam Armstrong into a starting XI that lost 2-0 to Wigan Athletic at the weekend.
The hosts were attacking early as Cauley Woodrow twice had chances from the edge of the Blackburn penalty area, Rovers goalkeeper Christian Walton up to the task on both occasions. Romal Palmer was next to have a go as Brown teed him up, but he blazed over the bar.
On 20 minutes, the Tykes had their best chance to break the deadlock, Alex Mowatt latching onto Eliot Simoes' lovely through ball in the box, but he was unlucky as his effort from 10 yards hit a defender's leg.
The first drinks break benefitted Blackburn as former Barnsley loanee Armstrong tested Tykes keeper Jack Walton with a simple shot after cutting in from the left before unleashing a low drive that Walton deftly turned away.
Brown came to the home side's rescue on the half hour as, after Jack Walton could only parry Stewart Downing's free kick, he cleared Johnson's header off the line. It got worse for Barnsley as Palmer picked up an injury and was substituted by Callum Styles.
Barnsley had the last chance of the half as Alex Mowatt fired from the edge of the area, Christian Walton denying him. Three minutes after the restart, Samuel should have put the visitor in front as he got free at the back post to meet Downing's free kick, but his volley somehow missed.
Struber made three changes with Ludewig, Luke Thomas and Chaplin replacing Simoes, Williams and Marcel Ritzmaier and it was two of those subs that powered Barnsley into the lead, Ludewig putting over a deep cross that Chaplin met and headed into the bottom corner past Christian Walton.
In the 74th minute, Brereton was sent off for intentionally tripping Ludewig and Barnsley took advantage soon after as Styles intercepted the ball, Mowatt eventually putting in a fine through ball that Brown finished low past the onrushing Christian Walton. No further chances meant the Tykes have taken seven points from nine since the return.
Man of the Match: Alex Walton
Not only did he keep a clean sheet, but when Barnsley were under siege in the first half, Walton was at his best to keep Blackburn off the scoreboard to give his side a chance, which they eventually took later in the game. The Tykes goalkeeper has now gone 294 minutes without allowing a goal and has kept a clean sheet in all three games since the season resumed.
Barnsley are headed in the right direction and seem on course to stay up despite still being in the bottom three. Their back line and goalkeeping is playing exceptionally well at the moment and their attack is generating just enough goals to grind out wins. With their next game being against strugglers Stoke City, the Tykes may very well make it three wins on the bounce.
Blackburn will seemingly be in the play-off chase until the end, but their current form has to worry Mowbray. They've been shut out in three of their last four games and their next three matches are against top of the table Leeds United, sixth-place Cardiff and second-place West Bromwich Albion, which will severely test Rovers as they enter the stretch run.