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, scored in the only competition in which he had failed to net after he was left all alone by Fredy Guarin's shocking pass-back six minutes before the interval.
Europa League holders Porto started brightly against the Champions League winners, with Hulk a lively presence up front for the Portuguese outfit. Aided by the busy Guarin, Porto rattled their illustrious opponents in the opening exchanges.
Porto was playing the Catalans at their own game, and every time Pep Guardiola's men ventured forward, they were caught out by their rivals' offside trap.
But it doesn't take long for Barca to figure out Porto.
Barca 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 teammate, was waiting all alone to pounce, leaving Helton grounded with a glorious feint and slotting into the empty net.
Flashback to 2003, Messi had missed a similar opportunity in his Barcelona debut, but this time he left the Portuguese team with an uphill task.
Barca was the better side and continued to attack in the second half and that pressure brought a rash challenge from Rolando, already booked, who then saw red after a cynical foul on Messi.
And the Catalans took quick advantage as Mess turned provider for Fabregas, who chested down Messi's pinpoint cross and volleyed past Helton to register his first goal in some style.
It could have been three after that, but Barca was comfortable in the end as they lifted a 12th title under Guardiola - and two in two games for Fabregas.