He was drafted one spot ahead of Albert Pujols at 401st overall in the 1999 Draft by the Anaheim Angels. In his first professional season with the Class-A Boise Hawks he hit.322 and was named to the Northwest League All-Star team. In 2000 with the Lake Elsinore Storm he hit.279, was an honorable mention selection to the California League All-star team and was second in the league with 73 stolen bases. In 2001 with the Double-A Arkansas Travelers he hit.312 in 70 games and was named to both the mid-season and postseason Texas League All-Star teams. He also was a member of the "World Team" at the All-Star Futures Game and was named the Angels Minor League Defensive Player of the Year. In 2003, he was named to the Pacific Coast League All-Star team, while leading all Angels minor leaguers with a.347 average for the AAA Salt Lake Stingers. Amézaga made his Major League debut on May 24, 2002, against the Minnesota Twins as a shortstop. He was hitless in three at-bats that day. He recorded his first Major League hit two days later, a double to left center against Twins pitcher Eric Milton. His first home run did not come until August 19, 2003, against Jon Garland of the Chicago White Sox. In three seasons with the Angels, he played in 122 games and hit.209. He also appeared in two games for the Angels in the 2004 American League Division Series against the Boston Red Sox, and was hitless in two at-bats.
Amézaga was designated for assignment by the Angels after the 2004 season and selected off waivers by the Colorado Rockies. He made the opening day roster with the Rockies, his first such achievement in the big leagues. He only appeared in two games for the Rockies and was one for three before the Rockies designated him for assignment on April 20.
He was claimed off waivers by the Pittsburgh Pirates and was 0 for 3 in three appearances with the Pirates. He spent the remainder of the season in AAA with the Indianapolis Indians, where he hit.341 in 64 games.
He signed as a free agent with the Florida Marlins prior to the 2006 season and appeared in a career high 132 games, hitting.260. He appeared in 417 games with the Marlins over four years, hitting.259 during that span. However, he underwent microfracture surgery on his left knee in July, 2009 and missed the rest of the season while recovering. The Marlins chose to release him after the season.
He was signed to a minor league contract by the Los Angeles Dodgers on February 2, 2010. Still recovering from his injury, he did not play in any spring training games. Amézaga made his season debut on May 17 for the Double-A Chattanooga Lookouts. He only had four at-bats before returning to the disabled list for the remainder of the season, after which he became a free agent.
Return to Colorado
Amezaga signed a minor league contract with an invitation to Spring training with the Colorado Rockies on January 26, 2011, but failed to make the team and was sent down to Triple-A Colorado Springs. He had his contract purchased on April 29. He was designated for assignment on May 29.
Return to Florida
On August 6, 2011, Amézaga was re-acquired by the Florida Marlins from the Rockies in exchange for minor league shortstop Jesus Merchan. He played 20 games for the Fish, batting.136 in 49 plate appearances.
He signed as a minor league free agent with the Chicago Cubs on January 13, 2012. He spent the season in AAA with the Iowa Cubs and hit.274 in 113 games.
Los Angeles Dodgers
He signed a minor league contract with the Dodgers on January 5, 2013, and was assigned to the AAA Albuquerque Isotopes. After hitting.339 in 37 games for the Isotopes, he was released on June 2.
On April 10, 2017, Amézaga signed with the Toros de Tijuana of the Mexican Baseball League. He was released on February 27, 2018. Amézaga announced his retirement as an active player following his participation in the 2018 Caribbean Series.
Coaching career
Amézaga was named as a coach for the AA Mississippi Braves in the Atlanta Braves organization for the 2019 season.
