Miller was traded to the Toronto Blue Jays on December 7, 2001 for Billy Koch. He made his Major League debut on April 12, 2002 for the Blue Jays against the Tampa Bay Devil Rays. He pitched innings of relief, hitting the first two batters he faced, and allowing a total of four hits and one run. He made his first ML start on April 27 against the Anaheim Angels, but lasted only innings while giving up four runs. He appeared in 25 games with the Blue Jays in 2002, starting 18 of them and finishing 9-5 with a 5.54 ERA. He missed most of the 2003 season with a shoulder injury and returned in 2004, when he appeared in 19 games for the Blue Jays and went 3-4 with a 6.06 ERA. He then spent most of 2005 with the AAA Syracuse SkyChiefs, appearing in only one game for the Blue Jays.
He signed as a minor league free agent with the Tampa Bay Devil Rays in 2006 and appeared in five games for their AAA affiliate, the Durham Bulls. He was then released and played for the Chiba Lotte Marines in Japan, pitching in twelve games.
Florida Marlins
After a three-game stint with the Philadelphia Phillies AAA affiliate, the Ottawa Lynx, Miller signed a minor-league contract with the Florida Marlins. He started the season at Triple-A Albuquerque and was recalled by the Marlins on May 19, 2007, after an injury to Ricky Nolasco. Although Miller had been a starter in previous seasons, the Marlins used him to fill a relief role, with former closerByung-hyun Kim taking Nolasco's spot in the starting rotation. The Marlins released him on October 3,.
San Francisco Giants
On November 1, 2008, the San Francisco Giants signed him to a minor league contract with an invitation to spring training. He made the Giants roster and appeared in 44 games out of the bullpen, 3-3, with a 3.18 ERA, for the Giants in 2009.
Miller was signed to a minor league contract which included an invitation to spring training by the Los Angeles Dodgers on December 4,. He was assigned to the Triple-A Albuquerque Isotopes to start the season. His contract was purchased by the Dodgers on May 27. He appeared in 19 games with the Dodgers, compiling a 4.44 ERA. He was designated for assignment on July 23. He cleared waivers and was reassigned to Albuquerque. In 32 games for the Isotopes in 2010, he had a 1.95 ERA. He was granted free agency on October 6.
On November 17, 2010, Miller signed a minor league contract with the Seattle Mariners. He was released by Seattle April 25, 2011.
Texas Rangers
Miller signed a minor league contract with the Texas Rangers April 29. He was later released by the Rangers on June 6, 2011.
Return to Dodgers
On July 4, 2011, Miller signed a minor league contract with the Los Angeles Dodgers. He pitched in three games for the Albuquerque Isotopes, walking four and allowing two runs in innings for a 10.80 ERA. He was released on July 25.
Death
Miller was found dead in his Palm Harbor home on June 26, 2013. A cause of death was not announced. He was survived by his wife of 15 years, Jessica, and two sons.
Tattoos
Miller was known for his many tattoos. In a move sometimes called the "Justin Miller Rule", Major League Baseball told Miller that he had to wear a long-sleeved shirt under his jersey whenever he was playing because hitters complained about being "distracted" by Miller's sleeve tattoos.
