Tate, who received the highest signing bonus ($6.25 million) in franchise history, has completed substance abuse counseling from his first positive test and was playing for short-season Eugene of the Northwest League when the suspension was administered.
Tate, 20, was credited 25 games by the Office of the Commissioner for time that he's already served while undergoing counseling. The 25 games that are remaining on his suspension will begin immediately.
"It's obviously disappointing ... he's a guy who has never got his career on track," said Padres general manager Jed Hoyer. "He has taken ownership of this. We hope this is a wakeup call for him."
Tate has been injured often since beginning his professional career in 2010 and, to date, has only 183 plate appearances in parts of two seasons.
Tate started the season with Class A Fort Wayne before suffering a knee injury after an outfield collision with teammate Everett Williams. He was hitting .316 in six games at the time of the injury.
He then reported to Peoria, Ariz., where the Padres have their Spring Training facility. Tate started counseling in Arizona while also rehabilitating his knee.
He was hitting .286 in 11 games with Eugene, including a 0-for-4 performance in his last game on Monday against Everett.
"He's played well in spurts this year," Hoyer said. "His performance has inspired hope."
Since he signed with the Padres, Tate has dealt with concussion-like symptoms, a sports hernia, a broken jaw and facial lacerations stemming from an ATV accident, a sprained left shoulder, a thumb injury and a viral illness that preceded his knee injury this season.
"You want your players playing," Padres manager Bud Black said. "It's a big interruption in his development."