Kawasaki agreed to a minor league deal with the Toronto Blue Jays on March 14, 2013. He started the 2013 season on the roster of the Triple-A Buffalo Bisons. Kawasaki was called up to the Blue Jays on April 13 when José Reyes was added to the disabled list. With his appearance for the Blue Jays on April 13, Kawasaki became the first Japanese-born position player to appear in a game for Toronto.
On April 21, 2013, Kawasaki batted in the leadoff slot for the first time in Toronto, scoring the game's first run against the New York Yankees. On May 26, in the final game of a 4-game series against the Baltimore Orioles, Kawasaki recorded his first MLB walk-off hit, with a 2 run double against Baltimore closer Jim Johnson. On June 21, Kawasaki hit his first MLB home run, a two-run shot off Baltimore reliever Tommy Hunter, which tied the game 6–6. The Blue Jays would win the game 7–6 to extend their winning streak to 9 games. Kawasaki, at 32 years of age, became the oldest player in Blue Jays' history to hit his first career home run, one year older than Ken Huckaby. Kawasaki was optioned back to Triple-A Buffalo on June 26 when Jose Reyes was activated from the disabled list.
Toronto recalled Kawasaki from Triple-A Buffalo on June 28 after left-fielder Melky Cabrera was placed on the 15-day disabled list with left knee tendonitis. Kawasaki made his first MLB start at second base in a game against the Boston Red Sox on June 30, 2013. Kawasaki was optioned back to Triple-A on July 13 to make room for Brett Lawrie. Kawasaki was recalled on August 14 after Colby Rasmus was placed on the disabled list. Kawasaki was ejected for the first time in his major league career on September 21, against the Boston Red Sox after being called out at first base by umpire Eric Cooper and then subsequently throwing his helmet to the ground. He recorded his first career 4-hit game on September 25, against the Baltimore Orioles. Kawasaki finished the 2013 regular season with a .229 batting average, 1 home run, and 24 RBI in 96 games. The Blue Jays declined his $1 million contract option on October 31, making him a free agent. Kawasaki was awarded the GIBBY award for Topic of the Year on December 10, 2013, for his postgame speech on May 26.
On December 24, 2013, it was announced that Kawasaki had signed a minor-league contract with the Blue Jays that included an invitation to spring training. He did not make the major league squad, and was assigned to Triple-A Buffalo. On April 13, Kawasaki was recalled when Maicer Izturis was placed on the disabled list. He was optioned back to Buffalo on April 19, when Jose Reyes was activated. He was recalled again on June 17 when Steve Delabar was optioned to Buffalo. Kawasaki saw regular playing time after his call-up and appeared in 82 games for the Blue Jays in 2014. He batted .258 with 17 RBI for the season. Kawasaki was sent outright to the Buffalo Bisons on October 1, 2014, and became a free agent on October 31.
Kawasaki's first son, Issho, was born on August 16, 2013, in Toronto.