Guillen apologized again during a news conference in Miami, saying he would do whatever he could to repair relations with Cuban Americans. Miami is home to a large Cuban community, many of whom are Cuban exiles.
Guillen told Time magazine he loves Castro and respects the retired Cuban leader for staying in power so long. But during the news conference, Guillen said his comments were misinterpreted.
"I was saying I cannot believe somebody who hurt so many people over the years is still alive," Guillen said.
Guillen's suspension will be without pay and takes effect immediately.
"I'm very sorry about the problem, what happened," he said. "I will do everything in my power to make it better. ... I know it's going to be a very bumpy ride."
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.
The Associated Press contributed to this report.