In 2004, Pinto was named the Cubs' minor league pitcher of the year, after going 11–8 with a Southern League-leading 2.92 ERA while pitching for the Double-A West Tenn Diamond Jaxx.

Pinto was acquired by Florida, along with pitchers Sergio Mitre and Ricky Nolasco, in the trade that sent outfielder Juan Pierre to the Chicago Cubs in 2005.

In four scoreless innings for the Marlins in 2006, Pinto struck out three and allowed two hits before being optioned to the Triple-A Albuquerque Isotopes on May 30.

In 2008, Pinto stepped back into his situational lefty role, but he has been used many times as a multi-inning reliever and was even considered for a rotation spot during spring training.

On April 20, 2022, Pinto signed with the Piratas de Campeche of the Mexican League, after nearly 8 years out of professional baseball.