All 12, including Bastardo, have accepted the suspension, Major League Baseball said.
The Phillies issued a statement on Monday saying:
"Obviously, the Phillies are very disappointed to learn of Antonio Bastardo's violation of Major League Baseball's Drug Program. We strongly believe in the Program and look forward to a time when performance enhancing drugs are completely out of baseball. Hopefully the sanctions announced today will bring us closer to that day. We respect the fact that Antonio has acknowledged his serious mistake and accepted his 50-game suspension."
Among the other 11 players who have accepted 50 game suspensions are All-Starts Nelson Cruz of Texas, Jhonny Peralta of Detroi and Everth Cabrera of San Diego.
Also on the list are New York Yankees catcher Francisco Cervelli and outfielder Fernando Martinez; Seattle catcher Jesus Montero; New York Mets infielder Jordany Valdespin and outfielder Cesar Puello; Houston pitcher Sergio Escalona; San Diego pitcher Fautino De Los Santos; and free agent pitcher Jordan Norberto.
The most high-profile person named in the Biogenesis case is New York Yankees star Alex Rodriguez.
He has been suspended through the 2014 season, but can appeal.
Milwaukee outfielder Ryan Braun, the 2011 NL MVP, agreed July 22 to a 65-game ban through the rest of the 2013 season for his role with Biogenesis, a now-closed anti-aging clinic outside Miami.
A total of 14 players were targeted in the drug probe. MLB's investigation was sparked in January when the Miami New Times published documents obtained from former Biogenesis associate Porter Fisher that linked several players to the clinic.