McCarthy fired his effort into the bottom left after Danny Higginbotham handled Christopher Samba’s volley.
Moments earlier, Sunderland's Dean Whitehead had his penalty saved by Brad Friedel after Samba had fouled Daryl Murphy inside the area.
Earlier this week Rovers’ manager Hughes said McCarthy was struggling with a lack of confidence but was confident that the Bafana Bafana striker would soon re-discover his form.
Hughes has left McCarthy, who has scored eight goals this season but has not found the back of the net since October, out of his starting line-up on several occasions.
Speaking after the game, Hughes said: “Benni is positive about his penalty taking. He was disappointed he didn't convert one against Wigan.
“But today even though Craig Gordon guessed right, Benni’s pace and power was too much.”
The defeat pushed Sunderland into the bottom three after Wigan’s surprise draw against Liverpool and moved Rovers to within three points of sixth-placed Aston Villa.