Casilla was originally signed by the Oakland A's on January 31, 2000, as an amateur free agent, and pitched from then through 2005 under the name of Jairo Garcia. During spring training in 2006 he revealed his real name to be Santiago Casilla, and that he had used false documents which listed him as three years younger than his actual age when he first signed in 2000.
Casilla pitched small parts of 2004, 2005, and 2006 for the Athletics as a reliever. In 2007, Casilla was recalled by the Athletics from Triple-A after going 2–1 with a 4.13 ERA with 29 strikeouts in 24 innings. He stepped into a bullpen that had Huston Street, Justin Duchscherer, and Kiko Calero on the disabled list. Casilla started off well, going 2–1 with 2 saves and a 0.45 ERA in his first 16 games. But he wound up finishing the season with a 3–1 record and a 4.44 ERA in 46 games. He pitched in the A's bullpen in the 2008 and 2009 seasons with mixed success.
At the end of 2009, he was granted free agency by the A's and signed a minor league contract with the San Francisco Giants for 2010. He made his Giants debut on May 21, 2010 against his former team in Oakland and remained with the team for the remainder of the season until they won the World Series. He returned to the Giants for 2011 as a member of the bullpen and took over as its closer after Brian Wilson went on the disabled list in August.
Casilla picked up his first career base hit, a bases loaded, two out RBI ground ball single between Diamondbacks first baseman Paul Goldschmidt and Aaron Hill on September 14, 2012.
On December 17, 2012, Casilla re-signed with the Giants for 3 years at $15 million.
On May 28, 2013, Casilla underwent knee surgery to remove a cyst and was placed on the 15-day DL.
Casilla works with a prototypical power pitcher repertoire, chiefly throwing a low to mid-90s two-seam fastball and a hard-breaking slider. He also occasionally mixes in a curveball and changeup. However, at times, he struggles with control of his pitches.