Matthew, 88, has presented the staple Saturday morning show for 27 years and the BBC faced fierce criticism after they announced in January that he would be leaving the station as a regular host.
The veteran disc jockey hosted a special farewell episode of the show this morning which featured a compilation of highlights from the programme's history.
Matthew's final appearance left listeners tearful and the BBC was slammed as "shameful" for axing the fan favourite.
Earlier this year, the broadcaster revealed a new voice would take his spot as presenter after Matthew suffered an "extended bout of ill health".
He later hit out at the decision and labelled their comments "balderdash" in an interview with the Daily Telegraph.
Today's show closed with Billy Fury's Last Night Was Made For Love and also featured tracks Elvis Presley's Ghetto and The Beatles' She's Leaving Home.
As the last track played out, Matthew said: "That 1962 top five hit by Billy Fury brings me to the end of my reign as presenter of Sounds Of The Sixties and I must say I've enjoyed every minute of my 27 years in this chair.
"I'm saddened to leave but I'll be back on Radio 2 in the near future with something new, so keep your eyes open for further information.
"This is your old mate Brian Matthew saying that's your lot for this week, see you again soon."
Listeners aired their dismay at his departure on Twitter, with James Reeve (@JamesHReeve) writing: "End of an era. Brian Matthew stands down from "Sounds of the Sixties." Another bit of our lives slipping away."
David Traynier (@DTraynier) posted: "Sad to be listening to the last ever Sounds of the 60s with the legendary Brian Matthew. I will miss the warmth of his voice."
Kevin Stirrup thanked Matthew, adding "you have been part of my life since a child with your music and knowledge".
Meanwhile several fans also hit out at the BBC, with Bryce Lawrence (@ScrumMachine) writing: "Shame on the BBC for ditching Brian Matthew time they gave listeners what they want."
J R Tyler (@jrTyler) posted: "Shameful treatment of Brian Matthew, SOTS and 3.4 million listeners," while Bill Hooper adding: "Brian Matthew just nailed his last ever Sounds of the Sixties. What a bittersweet belter! @BBCRadio2 - what a mistake you've made."
When they announced the presenter's departure in January, the BBC said they planned to run a series of special programmes with him in the future.