The site, in the San Joaquin Valley town of Keene, was also the center for Chavez's United Farm Workers union.
The home of the labor leader and Latino American civil rights activist sits on a 187-acre site known as La Paz.
"Today, La Paz joins a long line of national monuments, stretching from the Statue of Liberty to the Grand Canyon, monuments that tell the story of who we are as Americans," said Mr. Obama.
Chavez founded the United Farm Workers in the early 1960s. Before his death in 1993, he taught thousands of Latino farm workers how to write contracts and negotiate with growers for better pay and working conditions.
"It just isn't recognizing my father's life. It's recognizing the contributions of Latinos and immigrants and all of the hard work they've done and the contributions they make to this great land," said Paul Chavez, Cesar Chavez's son.
The president praised Cesar Chavez for making "our world a better place" by deciding to change it.
"Let us honor his memory. But most importantly, let's live up to his example," Mr. Obama said.