"I am not going to apologise for the actions that he took but I believe that it was a good gesture from your government to our country to allow him to return home to his family for humanitarian reasons," he said at Rangoon airport shortly before his departure.
However, Burmese dissidents say Senator Webb's trip could be seen as an endorsement of the poor treatment received by Ms Suu Kyi and more than 2,000 other political prisoners.
After his arrest, Mr Yettaw, said he had been sent by God to deliver a warning to Ms Suu Kyi that she would be assassinated.
Senator Webb said he had asked Burmese leaders to consider the release of Ms Suu Kyi and allow her to participate in the political process ahead of next year's elections, but that they had not yet responded.
Later he met the pro-democracy leader for talks lasting about 40 minutes. She was taken to a state guesthouse near her home to meet Senator Webb.
Senator Webb met Ms Suu Kyi after talks with Burma's military leader
Ms Suu Kyi went on trial in May after Mr Yettaw swam to her lakeside home with homemade flippers, evading guards.
She was charged with breaking the terms of her house arrest by sheltering Mr Yettaw and, after many delays, was sentenced on Tuesday to three years in prison.
Gen Than Shwe has ruled Burma since 1992
Although the sentence was commuted to 18 months' house arrest by Than Shwe, it ensures the opposition leader cannot take part in planned elections next year.
Ms Suu Kyi, 64, has spent 14 of the past 20 years under house arrest.
Senator Webb, who chairs the Senate Foreign Relations subcommittee on East Asia and Pacific affairs, has previously called for more "constructive" US engagement with Burma.
He said in July that the trial of Ms Suu Kyi would make this difficult.
The UN Security Council expressed "serious concern" following Ms Suu Kyi's conviction earlier this week and urged the release of all political prisoners, while the EU extended sanctions against Burma.
But Burma's neighbour China said the world should respect its laws.
Thai Prime Minister Abhisit Vejjajiva, who is the current chairman of the Association of South East Asian Nations (Asean) told the BBC that imposing sanctions could lead to problems and that it was important to take a balanced approach to dealing with Burma.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.