His voice quaking and tears welling in his eyes, the number two Democrat in the Senate also apologised to any soldiers who felt insulted by his remarks.
"Some may believe that my remarks crossed the line," the Illinois Democrat said on Tuesday. "To them I extend my heartfelt apologies."
"They're the best. I never, ever intended any disrespect for them."
The apology came a week after Durbin, the Senate minority whip, quoted from an FBI agent's report describing detainees at the naval base in a US-controlled portion of Cuba as being chained to the floor without food or water in extreme temperatures.
"If I read this to you and did not tell you that it was an FBI agent describing what Americans had done to prisoners in their control, you would most certainly believe this must have been done by Nazis, Soviets in their gulags or some mad regime - Pol Pot or others - that had no concern for human beings," the senator said on 14 June.
Durbin's Guantanamo comments
created a buzz on the internet
The comments created a buzz on the internet and among conservative talk radio hosts, but Durbin initially refused to apologise.
"This administration should apologise to the American people for abandoning the Geneva Conventions and authorising torture techniques that put our troops at risk and make Americans less secure," he said the day after his initial comments.
By last Friday, Durbin was trying to clarify his comments, yet the White House and top Republicans, including Senate Majority Leader Bill Frist, refused to relent.
Defence Secretary Donald Rumsfeld, in an interview scheduled for broadcast on Wednesday on Fox News Radio, tried to equate the comment with actress Jane Fonda calling US soldiers war criminals during a visit to North Vietnam in 1972.
On Tuesday, Chicago Mayor Richard Daley - a fellow Democrat - added his voice to the chorus of criticism, saying: "I think it's a disgrace to say that any man or woman in the military would act like that."
During his apology, which Durbin delivered while looking directly into a TV camera broadcasting the proceedings, the senator said: "I made reference to Nazis, to Soviets, and other repressive regimes. Mr President, I've come to understand that's a very poor choice of words."
"Some may believe that my remarks crossed the line. To them I extend my heartfelt apologies. They're the best. I never, ever intended any disrespect for them"
He also reached out directly to Holocaust survivors, adding: "I'm sorry if anything that I said caused any offense or pain to those who have such bitter memories of the Holocaust, the greatest moral tragedy of our time.
"Nothing, nothing should ever be said to demean or diminish that moral tragedy."
Immediately after the apology, Senator John McCain, an Arizona Republican and former prisoner of war, spoke in Durbin's defence.
"All of us, I believe, who have had the opportunity to serve in public life from time to time have said things that we deeply regret.
"I know that I have. I would like to say that the senator from Illinois, he did the right thing, the courageous thing, and I believe we can put this issue behind us."