Lovullo, in his first season with Arizona, managed the team to a 93-69 record -- 24 more wins than last season, the second largest win increase from 2016 among all teams -- and into the playoffs for the first time since 2011.
Lovullo built a culture of communication with the Diamondbacks. He often referred to the "love" teammates had for each other -- and Lovullo certainly loved the midseason deal that brought big-hitting J.D. Martinez to Arizona.
"We are going to be one year better," he said, adding that his club would be even "more united" in 2018.
Lovullo, 52, is the third manager in Diamondbacks history to win National League Manager of the Year, joining Bob Melvin in 2007 and Kirk Gibson in 2011.
Lovullo was the Boston Red Sox bench coach for four years before he was hired by the Diamondbacks.
Lovullo received 18 first-place votes and finished with 111 points total.
"It speaks for itself, when you get separated from the field like I did," Lovullo said on MLB Network. "There's a lot of great candidates."
Molitor managed the Twins to an 85-77 record. The team won 26 more games this year than last, the biggest increase in the major leagues. The Twins also became the first team to make the playoffs following a 100-loss season.
Shortly after the playoff loss to the New York Yankees, Molitor earned a new three-year contract to continue managing the Twins.
The 61-year-old Molitor was born and raised in St. Paul, Minnesota, and tallied the last of his 3,319 career hits with the Twins in 1998.
Molitor is the second person enshrined in the Baseball Hall of Fame as a player to later be named Manager of the Year, joining Frank Robinson.
"I was aware of some of the history," said Molitor, who received 18 first-place votes and 112 points.
The voting was much closer in the American League.
Information from the Associated Press was used in this report.