Sundowns were hoping to become the first side to lift the trophy three times, but instead AS FAR claimed that honour as they also became the first team to win the competition back-to-back.
The Moroccans collect US$600,000 in prize money, while Sundowns take home US$400,000, still a decent payday.
AS FAR also advance to the second round of the FIFA Women's Champions Cup 2027, where they will face North Korean side Naegohyang Women's FC in December.
Victory in that encounter would secure a place in the final phase in Miami, United States, where they would meet Mexico's Club América Femenil in the semi-finals in January.
AS FAR took the lead midway through the first half when Imane Touriss's shot from 25 yards took a deflection and beat Sundowns' experienced goalkeeper Andile Dlamini.
Sundowns were level just two minutes later when Botswana international Refilwe Tholakele curled in a superb equaliser from a tight angle.
But the South African side looked vulnerable at the back, and AS FAR regained the advantage when Hiba Youssoufi was given too much time and space in the box, allowing her to fire a shot that was again deflected past Dlamini.
Sundowns pushed for an equaliser but rarely troubled the Moroccan goal and were caught on the break as Touriss netted her second after excellent work from Fatima Tagnaout on the right wing.
Sundowns had been seeking revenge after losing the 2022 final 4-0 to AS FAR, a match in which they had two players sent off.