Pujols received all 32 first-place votes and 448 points in balloting, announced by the Baseball Writers' Association of America.
It was the third MVP award for the St. Louis Cardinals star, who also won in 2005. He became the first unanimous MVP since Bonds in 2002.
Pujols said he concentrates on World Series titles, not MVPs. He won his only championship in 2006.
"I always make a joke. I got 10 fingers. I want to get nine more rings," he said. "I want to get as many as Derek Jeter has so far [five]. Obviously that's hard to do."
Pujols does have one individual goal — the Hall of Fame.
"Obviously, there is still a long way to go," he said.
Pujols led the majors in home runs (47), runs (124), slugging percentage (.658) and intentional walks (44), and topped the NL in on-base percentage (.443). He was second in the league in doubles (45) and third in batting average (.327) and RBIs (135).
He was especially dangerous with the bases loaded, going 10-for-17 with five grand slams, three doubles and 35 RBIs.
"I think it was the most consistent year," he said. "I was pretty much hot April until almost September."
Florida's Hanley Ramirez, the NL batting champion, was second with 233 points, followed by Philadelphia's Ryan Howard (217) and Milwaukee's Prince Fielder (203), who tied Howard for the big league lead in RBIs.
Pujols didn't homer in his final 89 regular and postseason at-bats after Sept. 9. He had minor surgery Oct. 21 to remove a bone spur from his right elbow. He had feared he might need ligament replacement, causing him to miss the first half of next season.
"My elbow was fine," Pujols said. "I don't put that as an excuse. I was still playing every day out there."
Pujols, who turns 30 in January, joined Hall of Famer Al Simmons (11) as the only players with 100 or more RBIs in each of their first nine seasons. He also set a big league record for assists by a first baseman with 185.
Pujols became just the fourth player to win the NL MVP three times. Bonds won seven in the 1990s and 2000s. Stan Musial (1940s), Roy Campanella (1950s) and Mike Schmidt (1980s) each won three.
Five players have won three AL MVPs: Jimmie Foxx, Joe DiMaggio, Yogi Berra, Mickey Mantle and Alex Rodriguez.
In addition to Pujols and Bonds, the only unanimous NL winners were Orlando Cepeda (1967), Schmidt (1980), Jeff Bagwell (1994) and Ken Caminiti (1996). Unanimous AL winners have been Hank Greenberg (1935), Al Rosen (1953), Mantle (1956), Frank Robinson (1966), Denny McLain (1968), Reggie Jackson (1973), Jose Canseco (1988), Frank Thomas (1993) and Ken Griffey Jr. (1997).
St. Louis players have won 17 MVPs, second in the majors behind 20 for the Yankees. Pujols has been voted among the top 10 in nine consecutive years, finishing second in 2002, 2003 and 2006; third in 2004; fourth in 2001; and ninth in 2007.
Pujols receives a $200,000 bonus for winning the award. He is signed for next season at $16 million, and the Cardinals hold a $16 million option for 2011, so the sides may soon turn their attention to a contract extension.
Joe Mauer of the Minnesota Twins was voted the AL MVP on Monday, receiving 27 of 28 first-place votes.