McCarthy took his season's tally to 18, with goals on 58 and 68 minutes, before Nicolas Anelka set up a rousing finale with what turned out to be just an 88th minute consolation.
And this was all from the man who missed one of two penalties in the last minute of the reverse fixture at Ewood Park.
Wanderers could even have snatched a share of the spoils in injury time of this game, when Abdoulaye Faye's fine header was ruled out because he was marginally offside.
However, the fine margins of top-flight football mean that Blackburn continue their unbeaten Premiership run at the Reebok that has prevented the hosts claiming a victory since 1998.
The last five contests between these two rivals have produced only three goals and two goalless draws.
And this one had all the makings of something similar from a very early stage, with both defences living on Easy Street as the game lacked any kind of fluidity in either final third.
Morten Gamst Pedersen fired an early free-kick high and wide, before El-Hadji Diouf saw a deflected shot trickle tamely wide too.
Blackburn's Ryan Nelsen and Bolton's Faye were the stand-out defenders, dealing with what very little action came their way.
Faye made his mark on Rovers' fledgling striker Matt Derbyshire midway through the half with a fair, but a crunching tackle that took both man and ball. Nelsen on the other hand, impressed in the air as Bolton tried to up the tempo later in the half.
And if you had to plump for a better side in the opening 45, the hosts just shaded it on weight of possession. But it was certainly Rovers winger David Bentley who had the best chance in the 23rd minute.
Derbyshire capitalised on Tal Ben Haim's weak clearing header to lay on Bentley, who fired just over from the edge of the box with only Jussi Jaaskelainen to beat.
The second half then actually began in a similar way to the first - dull and dire - before Bolton's ten minutes of penalty madness gifted McCarthy the chance to claim his side's second Reebok victory in three years.
On 58 minutes it was Gary Speed at fault for clipping the ankles of Bentley on the right side of the box and then exactly ten minutes later it was the otherwise faultless Faye to blame for recklessly hacking down the former Porto striker.
McCarthy expertly tucked away the first into the bottom right corner, but he was a bit more fortunate with his second, with Jaaskelainen getting a hand on the ball before it nestled in the same corner.
Bolton tried their best to respond immediately when both Henrik Pedersen and captain Kevin Nolan had shots cleared off the line.
Pedersen's drive was forced away by Bolton's former transfer target David Dunn, before Nelsen added to his performance by deflecting Nolan's volley wide.
Anelka then fired a fine left-footed strike beyond Brad Friedel with two minutes of normal time remaining, before Faye nearly redeemed his penalty blunder with his late header.