Afonso Alves thought he'd won it for Boro when he fired a sweet strike past Paul Robinson 15 minutes from time.
But super sub McCarthy had other ideas, heading home Brett Emerton's corner deep into stoppage time, for his first goal since February.
Earlier, Jeremie Aliadiere and Roque Santa Cruz had both struck the woodwork, while Tuncay had a perfectly legitimate goal ruled out for offside.
At a rain-soaked Ewood Park, Rovers registered the game's first effort, when Carlos Villanueva's long-range strike was deflected wide for a corner, but it was the visitors who ought to have opened the scoring.
On nine minutes, Stewart Downing's cross was headed clear, Chris Riggott lumped the ball back into the box over a static Rovers defence, Tuncay was clearly offside but Aliadiere certainly wasn't. However, the Frenchman's volley came crashing back off the bar.
Rovers responded well, with Ewood debutant Vince Grella spotting the run of compatriot Emerton from the right, but the Aussie international was denied by the legs of Ross Turnbull at his near post.
Matt Derbyshire then fired wide from Santa Cruz's knock-down, before the Paraguayan striker came within a whisker of breaking the deadlock. Stephen Warnock slipped the ball through, but Santa Cruz's left-foot shot struck the inside of the post, before being put behind for a corner.
A goal did arrive just past the midway point of the half, only to be wrongly ruled out for offside. Didier Digard sent a looping header into the path of Tuncay, who fired an acrobatic overhead kick past Robinson, only to be denied by an incorrect linesman's flag.
The final chances of the half again fell to Santa Cruz, who sent a powerful header straight at Turnbull, before latching onto Villanueva's throughball, only to be denied by the keeper's oustretched arm.
The South American star suffered a blow to the head early in the second half, but received a rousing reception on his return to the field.
It was a Brazilian who next came closest, as Alves cut inside Ryan Nelsen, but his left-foot shot deflected off the Rovers skipper and just eluded the far post.
But it was a warning that wasn't heeded by the home side, as Boro broke through with their next attack. Gary O'Neil's long ball was brought down by Alves under pressure from Andre Ooijer and Boro's record signing smashed the ball past Robinson from the edge of the Rovers box.
Middlesbrough looked to have held out, until Rovers won a corner in the fourth and final minute of time added on. McCarthy just beat his own keeper Robinson to the ball and the South African striker headed into the corner of the net, sparking jubilant celebrations from home fans and players alike.