Beckham, a shortstop ranked by MLB.com as Tampa Bay's No. 4 prospect and No. 91 overall, received the 50-game suspension after his second violation of the Minor League Drug Prevention and Treatment Program for a drug of abuse.
The ban is effective immediately.
"I regret that my poor judgment resulted in me letting my teammates and the Tampa Bay Rays organization down," Beckham said in a statement released by the Rays. "I take full responsibility for my actions and I will use this experience to refocus my commitment to baseball. I recognize that I am blessed to be able to play baseball for a living."
Beckham is perhaps the most high-profile Minor League player to be suspended in recent years. Donovan Tate, who was the No. 3 overall pick in the 2009 Draft, was also suspended for a drug of abuse violation last June.
"I owe it to my teammates, my family, and to myself to respect the game and the responsibilities that go with playing it as a professional," Beckham said. "I am sorry."
Minor Leaguers are warned after testing positive for a drug of abuse and then suspended after a second violation. The Commissioner's Office does not disclose the specific substance in these cases. Substances considered "drugs of abuse" by Major League Baseball include cocaine, marijuana, heroin, LSD, ecstasy and other opiates.
Beckham, 22, was on the 7-Day Disabled List with Triple-A Durham and hasn't played in a game since April 19. He's batting .204 with no homers and four RBIs in 13 games with the Bulls this season.
"We are very disappointed by Tim's actions," said Andrew Friedman, the Rays' Executive Vice President of Baseball Operations. "Tim possesses great potential, and he must rededicate himself in order to become the person and player we know he can be."
Beckham, drafted out of Griffin (Ga.) High School in 2008, has worked his way up the Rays' system but has failed to follow in the footsteps of fellow '08 draftees like Eric Hosmer and Buster Posey, who have reached the Majors.
He made his Triple-A debut in 2011, which was something of a rebound season for Beckham's prospect status. He split the season between the Bulls and Double-A Montgomery, batting .271 with a dozen homers, 70 RBIs and 17 steals.
Beckham is the 38th player to be suspended in 2012 for violation the Minor League drug program.