He spent the 2003 season with the Single-A Cedar Rapids Kernels, slashing .308/.346/.446 with 6 home runs and 57 RBI.

In 2004, Aybar played for the High-A Rancho Cucamonga Quakes, batting .330/.370/.485 in 136 games with career-highs in home runs (14) and RBI (65).

He recorded his first major League hit, in his first start, on May 20, 2006, against the Los Angeles Dodgers, a single to right field in the fourth inning off of Brett Tomko.

Aybar hit his first career major league home run on September 25, 2007, in a game against the Texas Rangers.

On September 5, 2009, Aybar tied a franchise record for most triples in a game with two against the Kansas City Royals.

On July 10, 2014, Aybar was named an All Star for the first time in his career, replacing injured Kansas City Royals outfielder Alex Gordon.

On November 12, 2015, the Angels traded Aybar, Sean Newcomb, Chris Ellis and cash to the Atlanta Braves for Andrelton Simmons and José Briceño .

On August 16, 2016, the Braves traded Aybar to the Detroit Tigers in exchange for Mike Avilés and Kade Scivique.

On February 17, 2017, Aybar signed a minor league contract with the San Diego Padres organization, receiving a non-roster invitation to spring training.

On April 18, Aybar made a pitching appearance for the Padres in a blowout loss against the Arizona Diamondbacks, and got catcher Chris Herrmann to hit into the final out of the game.