Mbappe opened the scoring in the 37th minute before Rodrygo doubled Madrid's lead early in the second half. Vinicius sealed a comfortable win for the Spanish and European champions with a late penalty.
France striker Mbappe returned to the Madrid line-up in Doha after missing Saturday's 3-3 draw with Rayo Vallecano due to a hamstring injury suffered in the Champions League win at Atalanta last week.
Mbappe swept in from close range to break the deadlock after brilliant play from Vinicius Junior, who won the FIFA Best men's player of the year award a day earlier after missing out on the Ballon d'Or.
Rodrygo's fine curling strike from the edge of the area put Madrid in total control, but the goal wasn't without controversy.
It was allowed to stand after the referee consulted the pitchside monitor even though Jude Bellingham was in an offside position and appeared to be interfering with the goalkeeper's line of vision.
Vinicius added a third from the penalty spot six minutes from time following another VAR review after Lucas Vazquez was chopped down in the Pachuca box.
This is the first edition of the FIFA-backed Intercontinental Cup, which broadly maintains the previous format of the Club World Cup.
The latter is being expanded to include 32 teams in 2025 and will now be played every four years. A past version of the Intercontinental Cup ran from 1960 to 2004 involving the champions of Europe and South America.
Madrid are to due to play Pachuca again at next year's Club World Cup in the United States, as well as an Al Hilal team featuring Neymar, and Red Bull Salzburg.
Carlo Ancelotti's side host Sevilla in La Liga on Sunday in their final game of the year. They will return to the Middle East in early January for the four-team Spanish Super Cup in Saudi Arabia.
© 2024 AFP