The suspension of Rowell, who is currently on the short-season Single-A Aberdeen IronBirds' roster, will be effective on June 18th.
The Orioles were attempting to convert Rowell into a pitcher at extended spring training after drafting him as a third baseman in 2006. Rowell was the ninth overall pick, taken one spot ahead of pitcher Tim Lincecum.
Rowell batted .227 with 11 RBIs in 41 games at Double-A Bowie last summer after spending the three previous seasons at Single-A Frederick.
Rowell is the third Orioles minor leaguer since spring training to be suspended 50 games for a drug of abuse, joining catchers Brian Ward and Michael Olhman.
"I'm sure any time those things happen - I'm not going to get into comparing it to society - but if there's one (player), it's a concern. But unfortunately it's part of the world we live in and we try to keep it from happening," manager Buck Showalter said.
"I don't really care to how it compares to other organizations or society in general, numbers, ratio. I don't. I just don't want it happening with the Orioles. But I have children and I understand the challenges that are out there. I'm not condoning anything. We'll see."