He is Cuban-American and was nicknamed "Gonzo" in order to tell the difference between him and the other Alex Gonzalez, who signed with the Blue Jays on November 26, 2009; coincidentally, they would face each other in the 2003 National League Championship Series between the Marlins and Cubs.

After making the major league team to begin 1994, Gonzalez batted .151 in 15 games and was sent down to Triple-A Syracuse at the end of April because of a hamstring injury.

With Syracuse, Gonzalez batted .284 as he spent the rest of the season in the minors due to the major league strike and made the all star team.

After spending eight years with the Toronto Blue Jays, he was traded to the Chicago Cubs on December 21, 2001, for Félix Heredia and minor leaguer James Deschaine.

During the Cubs' eighth inning collapse in Game 6 of the 2003 NLCS versus the Florida Marlins, which became infamous due to the Steve Bartman incident, Gonzalez committed a fielding error on a ground ball in the hole hit by Miguel Cabrera, contributing to the Marlins scoring seven runs, five unearned, afterward in that inning.

He became a free agent after the season and signed a one-year deal with the Tampa Bay Devil Rays for 2005 as a third baseman, making the switch from shortstop.

But despite a strong showing in spring training during which he batted over .400, Gonzalez failed to make the Royals' 25-man roster prior to the 2007 season, and exercised his right to become a free agent.

Gonzalez has worked as an analyst for NBC Sports and MLB Network covering season news and the World Baseball Classic.