The Argentine gave Pep Guardiola's side the lead late in the first half and the club's most recent signing opened his account to secure victory close to the end
Messi, named European Player of the Year at Uefa's Champions League draw on Thursday, netted in the only competition in which he had previously failed to score after he latched on to Fredy Guarin's shocking pass-back six minutes before the interval. Fabregas then collected a pass from the attacker to control and lash into the roof of the net.
Europa League holders Porto started brightly against the Champions League winners, with Hulk a lively presence up front. Aided by the busy Guarin, Porto rattled their illustrious opponents in the opening exchanges and Moutinho's drive on the bounce tested Victor Valdes, while Hulk was off target with a low drive.
Porto were pushing up and pressing Barca, playing the Catalans at their own game, and every time Pep Guardiola's side ventured forward, they were caught out by their rivals' offside trap.
But it doesn't take long for Barca to figure out their rivals and Guardiola's men began to enjoy more of the possession as the game wore on.
Messi, who had started quietly and looked uncomfortable at times, almost set up David Villa following a fantastic run and pass through the heart of the Porto defence, but Romanian full-back Cristian Sapunaru got a vital touch and Helton came charging of his line to gather.
Xavi then came close with a fierce drive from the edge of the box, put Helton pushed the ball over the crossbar.
Barca were growing in stature, though, and soon took the lead as Guarin inexplicably played a back-pass into his area where Messi, who would have been offside had the ball been sent through by a team-mate, was waiting all alone to pounce, leaving Helton grounded with a glorious feint and slotted into the empty net.
After the break, Villa shot straight at Helton and Pedro was denied by the Brazilian keeper as he raced through on his own. Porto had a penalty shout turned down when Eric Abidal clattered into Guarin after losing control of the ball in the area, but the referee waved play on.
Barca were the better side, however, and continued to attack.
That pressure brought another rash challenge from Rolando, already booked, who then saw red after a cynical foul on Messi.
And the Catalans took quick advantage as Messi turned provider for Fabregas, who chested down the pinpoint cross and volleyed past Helton to register in some style. Guarin's late lunge on Mascherano, leaving the referee no choice but to send him off, concluded a miserable evening for the Portuguese.
It could have been three after that, but Barca were comfortable in the end as they lifted a 12th title under Guardiola - and two in two games for Fabregas.