"I wasn't surprised at all," Pujols said. "You have to consider everything. You have to put all the numbers together."
Los Angeles outfielder Manny Ramirez and Milwaukee pitcher CC Sabathia also drew strong support after being traded by AL teams in July.
Pujols got 18 of the 32 first-place votes in balloting by the Baseball Writers' Association of America and had 369 points. The first baseman added to the MVP award he won in 2005.
Howard, who led the majors with 48 homers and 146 RBIs for the World Series champion Phillies, drew 12 first-place votes and 308 points.
Milwaukee outfielder Ryan Braun was third with 139 points, with Ramirez fourth at 138. Houston's Lance Berkman was fifth and Sabathia sixth.
Brad Lidge, perfect on 41 save chances for the Phillies during the regular season, drew the other two first-place votes and came in eighth. Voting was completed before the playoffs began.
"There were so many candidates," he said on a conference call from his home in St. Louis. "I'm happy I didn't have to make that decision."
Pujols was remarkably consistent all year - a trait he's demonstrated throughout his career. He is the only big leaguer to hit at least 30 home runs in his first eight seasons in the majors, and has finished in the top 10 of the NL MVP voting each year.
Pujols, the only player on all 32 ballots, led the league in slugging percentage and intentional walks. He drew 104 walks while striking out only 54 times, and was second in the NL with a .462 on-base percentage.
Almost single-handedly, when the Cardinals' rotation was depleted by injuries, he tried to keep St. Louis in contention while batting .398 in the month of August.
In mid-October, Pujols had surgery for nerve irritation in his right elbow, an ailment that caused numbness, tingling in his ring finger and pinkie, a weak grip and pain inside his forearm. He hopes to resume weight training after Thanksgiving and is expected to be ready for spring training.
"The worst part was the last two months," he said.
Pujols said there was still a slight chance he might need Tommy John reconstructive elbow surgery.
"I'm crossing my fingers," he said.
Pujols became the 25th multiple MVP winner in either league. Howard got off to a slow start and was hitting under .200 toward the end of May. His best month came in September, when he set a team record with 32 RBIs in the month and helped the Phillies rally to the NL East title. Howard won the NL MVP in 2006.
Ramirez had 138 points. He hit .396 with 17 home runs and 53 RBIs after the Dodgers got him from Boston on July 31, and led Los Angeles' push to the NL West title.
Sabathia got 121 points. He was 11-2 with a 1.65 ERA after Milwaukee acquired him from Cleveland on July 6, and helped the Brewers win the wild-card spot.
Both Ramirez and Sabathia drew second-place votes. Phillies shortstop Jimmy Rollins, who won the NL MVP last season, did not receive a single vote this year.
Pujols earned a $200,000 bonus for winning the award. Ramirez got $75,000 and Braun got $50,000.
The AL MVP will be announced Tuesday. A close vote is anticipated, with Minnesota's Joe Mauer and Justin Morneau among the top contenders along with Boston's Dustin Pedroia and Kevin Youkilis.