Ruiz signed with the Toronto Blue Jays on December 17. He began the season playing with the Las Vegas 51s in the Pacific Coast League, where he was selected to play in the 2009 Triple-A All-Star Game. Through 114 games with Las Vegas, Ruiz was having one of the best offensive seasons of any player in the PCL, with a .320 batting average, 81 runs scored, 43 doubles, 25 homers, 106 runs batted in, 270 total bases, a .392 on-base percentage, and a .584 slugging average. His marks in doubles, RBIs, and total bases led the league, when he was called up to Toronto on Aug. 11. On Sep 6, Ruiz was selected as MVP of the PCL.
Ruiz was called up to the Blue Jays major league roster on August 11, replacing Alex Ríos, who was claimed on waivers by the Chicago White Sox. Toronto was in New York at the time, to face the New York Yankees at the new Yankee Stadium, only a few blocks from where Ruiz had grown up. After striking out in his first at bat, Randy hit his first home run of 2009 with the Toronto Blue Jays. Ruiz duplicated the feat the next day, homering in the second inning off ex-Jay A. J. Burnett. On September 6, 2009, in a game against the New York Yankees, former Blue Jay Josh Towers threw a ball up and in, that ran into Ruiz, and hit him in the face. He walked off on his own power, receiving a standing ovation and waving to the crowd. Randy Ruiz finished the 2009 season (in which he played only 33 games) with 10 HR, 17 RBI, and a batting average of .313.