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.
The gathering at the ballpark drew a large turnout, including two dozen TV cameras lined up along the back. Among those in attendance were Marlins President David Samson and president of baseball operations Larry Beinfest.
The political firestorm came shortly after the Marlins opened their ballpark last week in the Little Havana neighborhood of Miami. The team is trying to rebuild its fan base with the help of South Florida's large Cuban American population.
Guillen apologized over the weekend after the story broke, but some Cuban-Americans remained upset. One group planned a demonstration Tuesday before Guillen said he would fly to Miami.
Francis Suarez, chairman of the Miami city commission, said Guillen should be fired. Joe Martinez, chairman of the Miami-Dade County board of commissioners, said Guillen should resign.
Polarizing comments are nothing new for Guillen, who once used a gay slur referring to a reporter, defended illegal immigrants and just last week he said he drinks to excess after road games and has done so for years.