At the news conference, Guillen said his comments were misinterpreted by the reporter, and he doesn't love or admire the dictator.
"I was saying I cannot believe somebody who hurt so many people over the years is still alive," Guillen told the news conference.
But Guillen took responsibility for the uproar, and said it left him sad and embarrassed. He also said he accepted the team's punishment.
"I'm very sorry about the problem, what happened," said Guillen, who is only five games into his tenure with the Marlins. "I will do everything in my power to make it better. I know it's going to be a very bumpy ride."
Outside an entrance to the Marlins' new ballpark, about 100 demonstrators wanting Guillen's ouster shouted and chanted during the news conference. The team didn't consider firing Guillen or asking him to resign, Marlins president David Samson said.
"We believe in him," Samson said. "We believe in his apology. We believe everybody deserves a second chance."
With reaction to Guillen's praise of Castro escalating in South Florida, he left his team in Philadelphia and flew to Miami in an attempt at damage control. The Marlins and Phillies had the day off and resume their series in Philadelphia on Wednesday.
Guillen said he'll be there to apologize to his players - but he won't be in the dugout. Bench coach Joey Cora will be the interim manager.
"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."
Baseball commissioner Bud Selig said he supported the decision to suspend Guillen. He called Guillen's remarks "offensive to an important part of the Miami community and others throughout the world" and "have no place in our game."
"As I have often said, baseball is a social institution with important social responsibilities," Selig added in a statement. "All of our 30 clubs play significant roles within their local communities, and I expect those who represent Major League Baseball to act with the kind of respect and sensitivity that the game's many cultures deserve."
Samson said he expected no further punishment by Major League Baseball.
The suspension recalled the punishment given to Marge Schott, the late owner of the Cincinnati Reds. Schott so embarrassed baseball in the 1990s with her inflammatory racial remarks and fond recollections of Adolf Hitler that she was suspended from ownership duties for a season.
About 100 reporters, photographers and cameramen attended the news conference. Guillen sat alone at the podium and began in Spanish, speaking without notes for several minutes before taking questions. Shortly after he started, his voice wavered in the middle of a sentence, and he paused to take a sip of water and clear his throat.
"This is the biggest mistake I've made so far in my life," Guillen said. "When you make a mistake like this, you can't sleep. When you're a sportsman, you shouldn't be involved with politics."
The news conference lasted nearly an hour, with about 80 percent of it in Spanish. Guillen said he was suspended without pay, but Samson later said the manager will be paid and will donate the money to Miami human-rights causes.
The 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 largeCuban-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 said he drinks to excess after road games and has done so for years.
Guillen twice appeared on a radio show hosted by Venezuelan President Hugo Chavez in October 2005, when Guillen led the Chicago White Sox to the World Series title. At the time, Guillen said: "Not too many people like the president. I do."
Chavez is unpopular with many Venezuelans, especially those living in the United States.