The 71-year-old closed today's programme by telling his listeners that "the years together with you have not only been a pleasure but a privilege".
Earlier in the show, Prime Minister Gordon Brown paid tribute to the DJ, praising him for having "shaped the popular imagination of British viewers and listeners".
"Five decades at the very top of British broadcasting is a towering, indeed an unparalleled achievement," said a message from Brown played during the 8am news bulletin.
"As you move on from Wake Up To Wogan, I wanted to let you know how very dearly you'll be missed and how delighted we all are you'll be returning with another venture before too long."
Before closing the show with Anthony Newley's 'The Party's Over', Wogan thanked his listeners for allowing him to share their lives over the years.
"When you tell me how important I've been in your lives, it's fairly moving. You've been every bit as important in mine," he said. "If anybody embodies the generous, warm spirit of this country it's you, my listeners."
Wogan also expressed his hope that the breakfast audience will welcome new host Chris Evans "with the same generosity of spirit that you've always shown me". In February, Wogan will return to Radio 2 to host a new Sunday show.