The first Saudi side to reach the final, Al Hilal was led by two penalties from Salem Al Dawsari and a close-range strike from Luciano Vietto.
Al Dawsari opened the scoring with a penalty in the 3rd minute and Pedro equalized for Flamengo four minutes later.
However, Flamengo's hopes were hit when Gerson conceded a penalty and was sent off in first-half stoppage time, allowing Al Dawsari to grab his second.
With Flamengo reduced to 10 men for the second half, Al Hilal controlled the tempo and eventually scored the third. Vietto's close-range strike was set up by Al Dawsari, and despite a late goal from Pedro, it was not enough for Flamengo to avoid elimination.
Al Hilal will face the winner of Real Madrid's semi-final against Al Ahly on Wednesday in Rabat, for a chance to become the first Saudi side to win the Club World Cup.