South Africa international McCarthy scored a tap-in after 12 minutes for his seventh goal this season and fourth in four matches after a 24-goal haul last season.
And Hughes said: "There were some huge performances on our side and I just think we really deserved the victory against a very good, strong side.
"On the night we disappointed Portsmouth so many times that in the end they just got a bit disillusioned and realised there was nothing for them. That's got to be a credit to my players.
"I thought Benni McCarthy was absolutely magnificent. He had a little period at the start of the season where he wasn't anywhere near the levels I expect from him but he understood that and knew he needed to work harder.
"At first it was fitness that wasn't right but he had lost a bit of form as well. Now he's back to where he should be and I took a lot of pleasure watching him tonight.
"His retention of the ball and his work in tight areas was a joy to watch and he was always in there looking for scoring chances.
"I left him out a few times but he's responded to that in the right way. Happily, everybody else performed as well."
Hughes's joy was marred, however, by an injury to midfielder Aaron Mokoena, McCarthy's fellow South African, who collapsed on the pitch in the first half and was carried off on a stretcher with a suspected broken leg.
Hughes said: "It looks like something gave way in his leg and we're worried that it is a bad injury.
"We are having to wait until he's assessed to see how serious it is but it doesn't look good.
"When he first walked off for treatment it looked like just a bang but he's had a broken leg before."
England winger David Bentley also limped off with recurrence of a shin injury but Pompey were unable to prevent Blackburn's seventh successive win and revenge for the home defeat at Ewood Park in September.
Morten Gamst Pedersen clinched victory with a 76th-minute strike, rendering substitute Kanu's stoppage-time reply immaterial.
Pompey boss Harry Redknapp said: "We lost to a good side. Blackburn are on a good run like ourselves and are full of confidence with two good strikers and strong defenders.
"We couldn't get to grips with the first half and although we were on top in the second we needed to score early to get back in it.
"We let in two poor goals and missed some chances as well.
"It's a shame because I would have loved a cup run and that's why I fielded a strong side but I wouldn't really swap our league result at Blackburn for beating them in the cup.
"We need to bounce back now at Newcastle on Saturday but we should do because we are a good side.
"I changed the system at half-time because of the state of the game but it's not about systems it's about players."