The outspoken Miami manager received the club penalty Tuesday before speaking to reporters about his comments on Cuba's Fidel Castro.
The suspension by the team takes effect immediately. It was announced shortly before Guillen was to hold a news conference to explain his remarks, which caused a public backlash.
Guillen told Time magazine he loves Castro and respects the retired Cuban leader for staying in power so long. At least two local officials said Guillen should lose his job.
"The Marlins acknowledge the seriousness of the comments attributed to Guillen," read a statement from the team. "The pain and suffering caused by Fidel Castro cannot be minimized, especially in a community filled with victims of the dictatorship."
Only five games into his tenure with the Marlins, Guillen left his team in Philadelphia and flew to Miami to apologize at the Marlins' new ballpark. The Marlins and Phillies had the day off and resume their series in Philadelphia on Wednesday.
Outside the entrance to the ballpark, demonstrators shouted as the news conference began. Guillen began by speaking in Spanish.