The home success keeps Steve Kean's side on top of the Championship table.
The 36-year-old former Portugal international, a free summer signing from Braga, snatched all three points for his side with a close-range finish in the 85th minute to maintain Blackburn's 100% home record.
But it was cruel on Barnsley, who were the better side for long periods and took a deserved first-half lead through former Chelsea midfielder Jacob Mellis.
Jordan Rhodes maintained his impressive goalscoring since his £8million move from Huddersfield with an equaliser against the run of play on the stroke of half-time.
It was Rhodes' third goal in as many appearances for Rovers but the home side were fortunate to go in level at the break, while the visitors appeared good value for the point they had wrenched from them in the closing stages.
Defenders Grant Hanley and Martin Olsson, midfielder Mauro Formica and striker Ruben Rochina all returned to Blackburn's starting line-up, while Barnsley were unchanged from the side that drew with Blackpool on Saturday.
Blackburn goalkeeper Paul Robinson was forced into a sprawling early save to keep out Mellis' strike from the edge of the penalty area and Tomasz Cywka fired in two long-range drives as Barnsley signalled their intentions.
The home side responded when Hanley headed Morten Gamst Pedersen's corner over the crossbar in the 15th minute and Rhodes flashed a shot from inside the area just wide soon after.
Rochina's 20-yard effort was routinely saved by Barnsley goalkeeper Ben Alnwick, but it was Robinson who had to perform acrobatics when turning aside Barnsley striker Craig Davies' goalbound shot from outside the area in the 24th minute.
Visiting defender John Stones and forward Chris Dagnall both threatened in quick succession before Mellis gave Barnsley a deserved lead in the 32nd minute.
Dagnall slipped the ball inside from the right into the area and Mellis finished in style, crashing the ball into the top corner from 12 yards.
Barnsley were good value for their lead and midfielder Stephen Dawson spurned another chance in the 38th minute, but against the run of play Blackburn equalised on the stroke of half-time.
Pedersen flicked on Bradley Orr's free-kick into the area and Rhodes was quickest to react, pouncing on the loose ball to sweep home a similar right-footed finish high into the roof of the net.
Barnsley held the edge after the restart. Rochina blazed over the crossbar but at the other end visiting striker Dagnall went close with a header before goalscoring chances dried up.
Marlon Harewood replaced Davies while Rovers manager Steve Kean sent on Nuno Gomes for Rochina with 24 minutes remaining.
Teenager Stones was forced off injured in the 73rd minute before Harewood dragged a shot from the edge of the area wide and Rhodes' effort from an identical position was held by Alnwick.
Barnsley midfielder Kelvin Etuhu, on for Dagnall and up against his older brother Dickson in the Rovers' midfield, was just off target with a 20-yard shot, while Mellis was wayward from even further out.
But just as the visitors looked set to claim a point, Nuno Gomes popped up in the six-yard box to steer home a cross from countryman Fabio Nunes with five minutes left.
