In 2006, his first year at Single A, Pérez went 4–0 with a 1.38 ERA. During his tenure in the minors he had a 12–15 record with a 2.99 ERA in his first 3 seasons. On April 15, 2011 Pérez got his first call up to the Toronto Blue Jays. On May 28, Pérez recorded his first career win in a 14-inning game against the Chicago White Sox. Corey Patterson hit a solo walk-off home run to give him the win. After making 29 appearances out of the bullpen for the Blue Jays, Pérez made his first career start against the Oakland Athletics on August 21, 2011. Pérez got the win, pitching 6 innings and giving up just 1 hit and 2 walks. He struck out 4 batters and retired 15 straight batters to open the game. Pérez recorded the win for the Blue Jays against the Cleveland Indians on Opening Day, throwing 4 scoreless innings. The 16 inning game was the longest game in Opening Day history. After pitching to a 2-2 record with a 3.43 ERA in 35 relief appearances, Pérez was removed from a game against the Chicago White Sox on July 8. After the game it was determined that Pérez had torn his ulnar collateral ligament, and missed the rest of the 2012 season. On May 7, 2013, it was reported that Pérez was expected to return faster than the usual one-year recovery time associated with Tommy John surgery. Pérez was added to the Dunedin Blue Jays roster for a rehab assignment, and pitched two innings in relief on June 10. His rehab assignment was changed to the Triple-A Buffalo Bisons on August 28. He was activated from the 60-day disabled list by the Blue Jays on September 3 after the Bisons season ended, and the major league rosters expanded. Pérez made his first appearance of the 2013 season on September 4. Pérez had surgery on his left elbow in January 2014 to remove scar tissue. On March 20, 2014, he was released by the Blue Jays to make room for Matt Tuiasosopo. warm-up game
Pérez signed a minor league deal with the Atlanta Braves on March 31, 2014. Still recovering from his elbow injuries, he would not throw a single pitch for Atlanta's minor league affiliates, and became a free agent at the end of the 2014 season.
Second Stint with Blue Jays
On February 6, 2015, Pérez signed a minor league contract with the Blue Jays that included an invitation to spring training.
