Cardinals first baseman Albert Pujols was voted the MVP for the second time in his career. Pujols, who won the award in 2005, was the only player named on every ballot.
Gonzalez, who this month won his first NL Gold Glove Award, earned an eighth-, ninth- and 10th-place vote.
Gonzalez, a first-time All-Star this past season, hit .279 with 36 home runs and 119 RBIs in 2008, ranking fifth in the league in home runs and third in RBIs.
It's the second consecutive season he eclipsed the 30-home run, 100-RBI mark.
"I think he's always had a great feel for what he's trying to do each and every at-bat," Padres manager Bud Black said. "He studies pitchers, he's on video, he watches them during the game. He recalls previous at-bats. He has a great knack for his approach, every at-bat, pitch-to-pitch.
"He has an understanding of what a pitcher is going to try and do to him. ... He's able to, more often than not, win the battle."
What did Gonzalez mean to the Padres?
"Without him, I do not know where we would be," Black said. "He's played pretty much every day. He's been tremendous, with the power, the RBIs, the defense -- he's been an All-Star performer, no doubt. He's been our best player."
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.