Eckstein, who will turn 34 on Tuesday, is an eight-year Major League veteran who split time last season between Toronto and Arizona. He can earn an additional $150,000 in incentives.
Eckstein was the MVP of the 2006 World Series while with the Cardinals and spent four seasons with the Angels where his current manager, Bud Black, served as pitching coach.
"The biggest thing the Padres offered was opportunity," Eckstein said. "I wanted to play second base. It's something in my career that I've always wanted to do. That's what they were willing to offer."
Eckstein hit .265 last season between stints with the Blue Jays and Diamondbacks as a shortstop, a position he's primarily played in his career.
But not anymore.
Eckstein said Thursday that he walked away from more money to play the one position -- second base -- he grew up playing and broke into professional baseball playing before he was moved to shortstop.
"It's where I played all the way up to the big leagues. It's been something inside of me. ... I wanted to play my best position. It feels natural. I told my agent that I wanted a second-base job," said Eckstein, who spent the last month working out in Arizona, taking ground balls at second base.
Black said Eckstein will hit either first or second in the order.
General manager Kevin Towers has said all winter that he wanted to add middle-infield "protection" for the upcoming season, especially after the team traded shortstop Khalil Greene to the Cardinals in December.
That trade left the Padres without a true shortstop on their 40-man roster. With Eckstein now in the fold, Towers said newcomer Chris Burke and Luis Rodriguez will likely get the majority of time at shortstop with Rule 5 addition Everth Cabrera possibility getting some time there as well.
Eckstein, a two-time All-Star who has a career .351 on-base percentage, drew praise from Black during a conference call Thursday for his ability to handle the bat.
"He's a good player and he's going to bring an element to our club that we need," Black said. "Offensively, he has the knack of getting on base. He's a great handler of the bat. The way he goes about the daily grind of playing baseball is going to be great for our younger service-time players to watch."
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.