Santiago made his major league debut for the Tigers in 2002. Used mainly as a backup, he was still named to the 2002 Topps All-Star Rookie Roster. During his rookie season, Santiago hit first-inning lead-off home runs on consecutive days (June 3, 2002 and June 4, 2002). In the June 3 game, he hit a second home run in the seventh inning. In 2003, Santiago assumed the starting shortstop role for the Tigers.

During Santiago’s two seasons with the Mariners, he played in only 27 games, spending most of his time in the minor leagues for the Triple-A Tacoma Rainiers. While playing for the Rainiers, Santiago was selected as the team’s MVP and Best Glove in 2005. He was also selected as the 2005 Top Second Baseman for the Triple-A Pacific Coast League. However, Santiago was released following the 2005 season.

Santiago played in 43 regular-season games and started in 18 games for the American League Champion Tigers in 2006. He played shortstop, second base and third base and did not make an error in 205⁄3 innings of play. Santiago started at shortstop in Game 1 and Game 2 of the 2006 World Series.

Santiago played for the Cibao Gigantes in the Dominican Winter League in 2009 and 2010. He led the team to a second-place finish in the Dominican Winter League Championships in 2010 and was asked to play shortstop for the Escogido Leones on Team Dominicana in the 2010 Caribbean World Series, which the Dominican won as Santiago hit .316 at the plate.

On November 30, 2011, the Tigers re-signed Santiago to a two-year extension, which kept him on the team through the 2013 season.

With the return of Omar Infante in July 2012, Santiago lost his every day second base position. He still played some games as a pinch hitter and as a late-inning defensive replacement. He also started at second and shortstop when needed. In a July 2013 game versus the Toronto Blue Jays, Colby Rasmus slid into second base, slide-tackling Infante, who was injured and placed on the disabled list. Santiago was called into the game and finished it out, and played several more games at second base until Infante returned.

Santiago was a non-roster invitee to the 2014 Cincinnati Reds training camp, and he made the team as a reserve infielder. On September 27, he hit a walk–off grand slam in the 13th inning against Pittsburgh Pirates pitcher Bobby LaFromboise in what would be the last at–bat of Santiago’s Major League career. He elected free agency on October 30, 2014

Santiago signed a minor league deal with the Toronto Blue Jays on January 30, 2015. During a spring training game against the Atlanta Braves on March 15, Santiago broke his left collarbone. He was released on March 30. The Blue Jays re-signed him to a minor league contract on April 6. He started the season on the disabled list of the Triple-A Buffalo Bisons, and was released on July 24.