Pena becomes the third rookie to be named World Series MVP joining Florida Marlins Livan Hernandez in 1997 and Larry Sherry with the 1959 Los Angeles Dodgers.
He also becomes the first rookie position player to be honoured.
It was a spectacular postseason performance from the Dominican, who delivered defensively and at the plate, registering at least one hit in each of the six World Series games.
Pena, who was also named the American League championship series most valuable player, added another line in the record books in Game Five when he became the first rookie shortstop to hit a home run in the World Series.
He also contributed a pair of hits in Game Six, scoring on Yordan Alvarez's sixth inning three-run blast that powered Houston into a 3-1 lead they would not surrender.
Houston took the best-of-seven series 4-2.
