On October 31, 2003, the San Francisco Giants signed Joaquín as an amateur free agent. His first professional experience came with the Dominican Summer League Giants in 2004; in 14 games, he had six wins and a 1.61 earned run average. He pitched for the Arizona League Giants in 2005, posting a 1-1 record with a 3.64 ERA, 37 strikeouts, and 10 walks in innings. He did not play in 2006 due to surgery on his right elbow, but he returned in 2007, for the Salem-Keizer Volcanoes of the Single-ANorthwest League, with whom he went 3-0 with a 2.84 ERA, 30 strikeouts, and 16 walks in 38 innings. In 2008, Joaquín played for the Single-A Augusta GreenJackets of the South Atlantic League and the Single-A advanced San Jose Giants of the California League. He was had a combined 1-3 with a 4.42 ERA in innings over 36 games. Joaquín began 2009 with the Double-AConnecticut Defenders of the Eastern League. He had a 4-5 record, a 2.67 ERA, 40 strikeouts, and 28 walks in 54 innings pitched. On August 1, Joaquín was called up to the Giants' bullpen; he replaced Ryan Sadowski on the roster. He made his Major League debut on August 4, giving up one run on two hits in pitching the ninth inning in an 8-1 win over the Houston Astros. He was optioned to the minors the next day to make room for Joe Martinez on the roster. Joaquín spent the rest of the minor league season with the Triple-AFresno Grizzlies of the Pacific Coast League; in eight games, he had a 1-0 record, an 0.00 ERA, 16 strikeouts, and two walks in 10 innings pitched. He was called up again on September 1 when rosters expanded, and he made nine more appearances for the Giants that year. In 10 games with the Giants, Joaquín had no record, a 4.22 ERA, 12 strikeouts, and seven walks in innings pitched. Joaquín made the Giants' Opening Day roster in 2010. He threw a scoreless of an inning in his first outing, but he gave up runs in each of his next three outings. At the beginning of May, he was sent down to Fresno when Aaron Rowand came off the disabled list. He was called up again on May 27 following an injury to Jeremy Affeldt, but he was sent down days later without making an appearance. In four games with the Giants, Joaquín had no record, a 9.64 ERA, two strikeouts, and seven walks in innings pitched. He was left off the postseason roster as the Giants won the 2010 World Series against the Texas Rangers. After the 2010 season, the San Francisco Giants removed Joaquín from their 40-Man Roster and placed him on release waivers. On November 22, 2010, Joaquín was claimed off of waivers by the Chicago White Sox. Joaquín refused the waiver claim and became a free agent. He was re-signed by the Giants in December 2010. In the 2011 season, Joaquín appeared in 5 major league games for the Giants, posting a 1-0 record and a 4.26 ERA in 6.1 innings, with 3 strikeouts and 3 walks.
Washington Nationals
He became a free agent on November 30, 2011, and subsequently signed a minor league contract with the Nationals on December 14.
