Emile Heskey had given the visitors an early lead with a powerful right-foot shot, before David Bentley equalised on the stroke of half-time.
Both managers were forced into a change apiece ahead of the game - the injured Shabani Nonda was replaced by Francis Jeffers in Rovers' attack, while Matt Jackson was tasked with marking the former Arsenal striker, coming in for the unwell Fitz Hall at the back.
Rovers arrived at Ewood Park on the back of two successive clean sheets, but they found themselves a goal down with less than two minutes on the clock.
Emmerson Boyce was played clear down the right flank and from his early ball in across the face of goal, Heskey got in front of his man and fired the ball past Friedel from six yards out.
Two minutes later and Rovers were handed a golden opportunity to equalise and from an almost identical move. Bentley fired across for McCarthy from the right, but the South African star didn't quite connect and toe-ended the ball wide.
Moments later and the former Porto striker again engineered himself a chance. The ball was played into his feet on the left side of the box and after an exquisite first touch, he fired a left-foot shot agonisingly wide of Chris Kirkland's far post.
Midway through the first half and again McCarthy threatened the visitors' goal. After being put clean through, the 28-year-old forced Kirkland to parry clear under pressure from the retreating defence.
Straight up the other end and Henri Camara twice went close within the space of a minute. The Senegalese striker volleyed straight into the arms of Friedel, despite a suspicion of handball, before firing across goal after a mistake by Zurab Khizanishvili.
On 33 minutes, Jeffers almost set up McCarthy after he had been played clean through by a defensive slide tackle, but the Merseyside man did turn provider on the stroke of half-time.
The Wigan defence were outfoxed after Bentley let the ball run through his legs and from Jeffers' immediate return pass, directly into Bentley's run, the England Under-21 international struck a delightful right-foot curler into the far corner of the net.
Making only his third start of the season, Jeffers twice went close early in the second half. Arjan De Zeeuw prevented a strike on goal with a last-ditch tackle, before Bentley almost fed Jeffers, only for Kirkland to smother the ball at the former England striker's feet.
That turned out to be Jeffers' last major involvement in the game, as he was soon to be replaced by former Wigan striker Roberts and the switch ultimately proved dividends.
But it was debutant Brown who proved to be the initial hero on 76 minutes. Andre Ooijer brought down Heskey inside the box and the Welshman produced a triple save to keep Rovers' hopes of maximum points still alive.
After saving substitute Svetoslav Todorov's poorly-struck spot-kick low to his right, he then repelled the Bulgarian's follow-up with his legs, before plucking Lee McCulloch's header out of the air on the line.
And with just nine minutes remaining, the script was set for the home side to steal the winner. From a long clearance over the top, Roberts won the race to the ball, his faint touch took it past Kirkland and McCarthy was left with the simple task of tapping the ball into the empty net for his fifth of the campaign.
As the game entered injury time, Roberts and McCarthy both had glorious opportunities to make the points safe, but a goal apiece from Thursday night's UEFA Cup heroes was enough to see Rovers move up to ninth in the table.