Hughes was only installed as Rovers boss on Thursday but he obviously knew his players well enough to make a substitution in the 59th minute that would secure this victory.
Matt Jansen has been out of the first-team picture for over six months but, brought in from the cold under Hughes' new regime, he climbed off the bench to lash home a much-needed winner for the home team.
Blackburn had dominated the second half but Portsmouth could and probably should have taken at least a point from the encounter, with strikers Ricardo Fuller and Yakubu both wasting great opportunities.
The winning goal came in the 76th minute. Lucas Neill drove forward and passed to Jansen who span away from Dejan Stefanovic before firing a left-footed shot beyond Shaka Hislop.
It was no more than Rovers deserved as, after a static first-half showing, they took control over out-of-sorts Pompey in the second period.
The first half was notable only for a worrying injury to Blackburn centre-back Craig Short following a tackle on Yakubu and also a drive from home skipper Barry Ferguson that flew just past the angle.
For the visitors, playmaker Eyal Berkovic limped off to be replaced by Steve Stone and Fuller really should have given them the lead after skipping past three Rovers defenders only to hit the post.
After the break it was a different story as, helped by the piercing runs of Brett Emerton and Paul Dickov's non-stop endeavour, Blackburn gained a stranglehold on the match.
First to go close was substitute centre-back Lorenzo Amoruso, whose rasping effort from a free-kick was turned aside by Hislop and Dickov could not quite convert the rebound.
Andy Griffin was booked for a terrible tackle from behind on Morten Pedersen and that sparked the arrival of Jansen, on in place of the ineffective Norwegian, and that instantly lifted the crowd.
Both Jansen and Emerton had efforts off target before new loan signing, Jay Bothroyd, joined the fray for the ineffective Jonathan Stead.
Even so, it was Brad Friedel's goal which should have been breached first, Yakubu shaking off the attentions of Dominic Matteo only to blast a golden opportunity into the fans behind the net.
However, after Bothroyd turned sharply and fired over, Jansen gleefully pounced to send the Rovers fans into raptures.
Portsmouth's goal survived further damage despite chances for Emerton, Dickov and Matteo before the visitors were unlucky from the most controversial moment of the game.
Hughes' predecessor at Blackburn, Graeme Souness, often bemoaned refereeing decisions when he was in charge at Ewood Park but Rovers were extremely fortunate when Friedel bundled Fuller over in the box three minutes from time.
It seemed a definite penalty but the Jamaican was booked for diving.
MAN OF THE MATCH: Paul Dickov (Blackburn) - The former Leicester forward's irrepressible running upset Dejan Stefanovic all afternoon and he was at the hub of all of the home side's best work.