The South Africa international, who had earlier missed a penalty, pounced to score his ninth goal of the season three minutes from the end of this pulsating derby.
In fairness that was the least Rovers deserved after a courageous second-half fightback, and Sam Allardyce's side might even have snatched an unlikely victory right at the death when Ryan Nelsen's header rebounded off the base of the post with Jussi Jaaskelainen stranded.
After a scrappy start, the game burst into life when Bolton drew first blood in the 15th minute courtesy of Matthew Taylor.
On-loan striker Ariza Makukula got in behind the home defence on the right-hand side of the area and his low cross-shot flashed across the face of goal towards the far post, where Taylor was lurking to apply the finish.
That was Wanderers' first goal in 462 minutes of top-flight action and Taylor's sixth of the season in all competitions.
Things got even better for Wanderers 20 minutes later when former Rovers striker Kevin Davies doubled the visitors' advantage.
This time Gretar Steinsson delivered a low cross from the right and, although Davies' initial shot was brilliantly saved by Paul Robinson, the Bolton striker reacted quickly to slam in the rebound from four yards out.
In contrast, Rovers offered precious little going forward and their only real chance of note in the opening 45 minutes was a speculative half-volley from Keith Andrews that flew narrowly wide on the stroke of half-time.
Desperate to inject more urgency into his side, Allardyce threw on Roque Santa Cruz and Tugay early in the second half and Rovers suddenly looked far more dangerous as a result.
Stephen Warnock halved the deficit in the 66th minute when he latched onto an exquisite throughball from McCarthy before steering a rising drive past Jaaskelainen.
Then, four minutes later, Rovers were awarded a penalty when Jaaskelainen flattened Santa Cruz in the area, but the Finn promptly atoned for his error by diving to his right to save McCarthy's spot-kick.
In the closing stages Rovers bombarded the visitors' box in search of an equaliser and it finally arrived in the 87th minute, McCarthy slamming the ball home from close range following good work by Chris Samba and Jason Roberts.