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Fabregas, who moved from Arsenal in a 29 million euro deal earlier this month, was on target two minutes from time after coming on as a substitute just eight minutes earlier.
Lionel Messi had put Barcelona ahead in the 39th minute as the Spanish giants added the European Super Cup to their domestic Super Cup triumph of last week.
Porto, the Europa League winners of last season, ended the match with nine men after Jorge Rolando and Fredy Guarin were red-carded in the closing stages.
Fabregas's goal was a strike to remember, as was the build-up.
Messi chipped the ball over a line of defenders into the path of Fabregas who calmly controlled it on his chest before volleying coolly past Helton in the Porto goal.
It was Fabregas's first goal since he scored for Arsenal against Huddersfield in the FA Cup back in January.
"Thank u all for your great support. And all i can remember in this moment is in what Arsenal has done for me in my career. Always in my heart," Fabregas wrote on his Twitter account after Barcelona had won a second Super Cup in three years.
It was Messi who had given Barcelona a first-half lead as he stamped his authority on the match at the Stade Louis II.
Porto lost the ball in midfield which allowed Messi to glide one way, then the other to deceive Helton and slot his opportunity home.
Barcelona midfielder Andres Iniesta said the win was the best way to go into the new Spanish league season which starts this weekend.
"We faced a rival team who were very physical, but we made the most of our chances," he said.
"It's a great joy to win this as well as the Spanish Super Cup. It's the best way to start the season."
The Portuguese side, who had won their domestic league without losing a game last season, had two opportunities in the opening 45 minutes, both from free-kicks.
But Brazilian striker Hulk, who scored 35 goals in that campaign, missed the target on both occasions.
Porto, now coached by Vitor Pereira after former boss Andre Villas-Boas switched to Chelsea in the summer, were the better side in the early stages of the second half with Victor Valdes pulling off a fine save to deny a long-range Guarin effort.
Messi then had the ball in the net only to be whistled up for offside before Barcelona showed off their strength in depth by introducing new signings Alexis Sanchez, their 26 million euro Chilean striker, as well as Fabregas off the bench.
Sanchez looked lively, curling a right-foot effort just wide of the post.
Porto's misery was complete when Rolando was sent-off for chopping down Messi in the 86th minute before Gurain also saw red in the 90th minute for a foul on Javier Mascherano.
"In a match of such intensity, it's normal that mistakes are made," said Pereira.
"It was because of this that we conceded the first goal. We forced Barcelona to make mistakes but we couldn't capitalise on it."
