He batted .351 with 7 home runs and 25 RBI in 35 games with Albuquerque, and he was promoted back to the Major Leagues on July 7, when the Marlins placed Josh Willingham on the disabled list.

He spent the rest of the season in the Major Leagues, mainly as a pinch hitter; he started only 12 games all year, most of them while Encarnación was injured.

Toward the end of the season, teammate A. J. Burnett ripped Marlins manager Jack McKeon for several reasons, one of which was that McKeon gave most of the available playing time to aging veterans, rather than to younger players such as Aguila, Willingham, and Jeremy Hermida, who had proven themselves already in the minor leagues, but had not received extended playing time in the Majors.

Also, Encarnación became a free agent following the 2005 season, and Juan Pierre was traded to the Chicago Cubs, so Aguila was put in a position to compete for a starting job in the Marlins' outfield in 2006.

After a second stint with the Marlins, he returned to Albuquerque for the rest of the Isotopes' season, where he finished the year there with a .318 batting average, 11 home runs, and 59 RBI in 77 games.

[5] He did not start any more games for the Marlins in 2006 after returning to the majors, but he did hit 2-for-3 with a single and a double in their season-ending win against the Philadelphia Phillies.

Since he was out of options on his contract, he needed to make the Marlins' opening day roster in 2007 in order to remain in their organization for a 10th season.

[7] Instead of remaining with the Marlins, he signed a minor league contract with the Pittsburgh Pirates on December 10, 2006, with an invitation to spring training.

[8] He joined the Pirates in spring training as a non-roster invitee, but did not make the team out of camp; and played for their Triple-A club, the Indianapolis Indians, where he hit (.250/.291/.360/651 in 172 at bats).

[11] He signed as a free agent with the Toronto Blue Jays on March 15, 2010 but after 44 games with the Las Vegas 51s, he was traded to the Philadelphia Phillies.