McCutchen captured 28 of the 30 first-place votes, finishing with 409 points. Goldschmidt was second with 242 points. He had 15 second-place votes and nine third-place votes.
St. Louis catcher Yadier Molina finished third in the voting with 219 points, garnering the other two first-place votes that McCutchen didn't earn.
Goldschmidt, who was seeking to become the first MVP in franchise history, led the NL in home runs (36), RBIs (125), total bases (332) and OPS (.952).
The American League MVP went to Tigers third baseman Miguel Cabrera for the second consecutive season.
"It's a huge honor just to be one of the finalists," Goldschmidt said in a release. "There have obviously been a lot of great players, just to be mentioned alongside them is a huge honor. I want to say congratulations to Andrew McCutchen and Miguel Cabrera and all of the other winners. It was a good year and hopefully we'll move on and get a little bit better as a team next year and strive towards making the playoffs and winning the World Series."
His second-place finish was the highest for the D-backs, as Matt Williams, newly hired manager of the Nationals, and Luis Gonzalez finished third in 1999 and 2001, respectively. More recently, outfielder Justin Upton came in fourth in 2011.
Many surmised that the vote was expected to be closer, and that the only thing separating Goldschmidt from McCutchen and Molina was that they played on teams that advanced to the postseason.
Goldschmidt was named to his first All-Star team in 2013, and earlier this month he took home his first Gold Glove Award. He finished the year with a .302/.401/.551 slash line, leading the league with the .551 slugging percentage.
Goldschmidt, who made his Major League debut in 2011, hit .286 with 20 home runs and 82 RBIs in his first full Major League season in 2012. The D-backs were so convinced they had a franchise player that they gave him a five-year contract extension in March that could keep him in Arizona through 2019.
"He's good at preparation, before, during the game and after. He's a great teammate. He works really hard," D-backs manager Kirk Gibson said during the season. "He has high expectations. He has high aspirations to be a world champion. He would never change. He'll never change until he stops playing. We've talked about the 'Diamondback Way' the last couple of years several times, and he's the model Diamondback guy. The model guy."
Goldschmidt's rise toward MVP consideration really started in May, when he hit .376. He was consistent, hitting seven home runs apiece in May, June and August. He finished strong, hitting .318 with 34 hits in the last month of the season.
Last week, Goldschmidt followed his Hank Aaron and Gold Glove Awards by winning a Silver Slugger Award. It's Goldschmidt's first silver bat, an annual honor for the best offensive player at each position in each league, as voted on by coaches and managers.
Goldschmidt has also been nominated for two Greatness in Baseball Yearly Awards (GIBBY) -- one for NL MVP and in the best-hitter category. Fans can vote as many times as they want through Dec. 2.