It was Farina's second violation, and he becomes the fourth player this year to be suspended under the Minor League Program. Last year, there were 105 suspensions in the Minors and an additional eight at the big league level.
Farina became susceptible to this type of suspension after he was removed from the Blue Jays' 40-man roster last season. Players who are on the 40-man roster cannot be tested for drugs of abuse.
"It's probably similar to Jeremy Jeffress a little bit," Blue Jays general manager Alex Anthopoulos said in reference to the pitcher who has tested positive for the use of marijuana in the past. "So when you're off the 40, there are implications.
"We definitely don't condone it, we're not happy about it. He's certainly embarrassed about it and he's going to have to learn either way. It's part of the game, and it just shows you that the program Major League Baseball has in place is certainly working."
Farina was limited to 24 1/3 innings last season as he made his way back from Tommy John surgery. He went 1-2 with a 5.18 ERA while striking out 24 and walking 14.
The 26-year-old was originally selected by Toronto in the third round of the 2007 First-Year Player Draft. His best season came in 2010, when he posted a 1.24 ERA at Class A Dunedin and a 1.40 mark for Double-A New Hampshire.
The suspension is set to begin at the start of the Minor League season. Fellow pitching prospect Marcus Stroman also will begin the year on the suspended list after he tested positive for a banned substance in September.