The European champions were pushed all the way by the Copa Libertadores holders before goalkeeper Matvey Safonov proved decisive from the spot.
PSG thought they had taken an early lead in the ninth minute when Fabian Ruiz turned the ball into an empty net after Flamengo goalkeeper Agustin Rossi struggled to deal with a corner. However, a VAR review ruled the ball had narrowly gone out of play before the finish.
Luis Enrique's side eventually broke the deadlock eight minutes before half-time, again capitalising on a mistake from Rossi. Desire Doue's low cross appeared to be running too fast for Khvicha Kvaratskhelia, but a touch from the Flamengo goalkeeper redirected the ball straight into the Georgian's path for a simple tap-in.
Flamengo, who had beaten Cruz Azul of Mexico and African champions Pyramids to reach the final, stayed in the contest and were rewarded on the hour. VAR confirmed Marquinhos had fouled Giorgian de Arrascaeta in the area, and Jorginho calmly converted the penalty, sending Safonov the wrong way.
PSG pushed hard for a winner, introducing Bradley Barcola and Ousmane Dembele late on. Dembele created an opportunity in stoppage time, but Marquinhos could not react quickly enough as the ball flashed across goal.
Extra time brought few clear chances, although Dembele went close in the 116th minute. The match was settled in the shootout, where Safonov, deputising for the injured Lucas Chevalier, made crucial saves to seal the trophy.
"We can be proud of ourselves; we played a great match against a tough opponent," said midfielder Warren Zaire-Emery. "Now, we have to keep this momentum going because the toughest part of the season is still ahead."
Luis Enrique praised his squad's historic year, saying: "I think it's impossible for Paris Saint-Germain to replicate this year. Six trophies is quite an achievement."
The victory completed a remarkable 2025 for PSG, who have now added the FIFA Intercontinental Cup to their UEFA Champions League, Ligue 1, Coupe de France, UEFA Super Cup and Trophee des Champions successes.
Paris Saint-Germain sporting director Luis Campos has said the club's owners are determined to extend Luis Enrique's contract, underlining how central the head coach is to their long-term plans.
Paris Saint‑Germain and Brazil's Flamengo have completed their final preparations in Doha ahead of the 2025 FIFA Intercontinental Cup final.
Marseille have taken another stride in Ligue 1 with a 1-0 victory over Monaco, propelled by Mason Greenwood's stunning finish and punctuated by coach Roberto De Zerbi's high praise for the English striker's long-term potential.
Bottom club Metz face a pivotal test in their battle to stay in Ligue 1 when reigning champions Paris Saint-Germain visit Stade Saint-Symphorien on Saturday.
