The former Two and a Half Men star took his time on stage to send a message to the cast and crew of the CBS sitcom.
"Before I present 'Outstanding Lead Actor in a Comedy Series' - my old category - I want to take a moment to take say something," Sheen said.
"From the bottom of my heart, I wish you nothing but the best for the upcoming season," the actor concluded.
He went on to present Big Bang Theory star Jim Parsons with the award.
Sheen was fired from Two and a Half Men in March after engaging in a very public feud with show creator Chuck Lorre.
He recently admitted that he would have fired himself from the series for his antics as well.
Two and a Half Men returns tomorrow evening on CBS, with Ashton Kutcher in the lead role of internet billionaire Walden Schmidt.
More from the Primetime Emmy Awards 2011:
> Primetime Emmys 2011: Ricky Gervais jokes that he is 'not allowed on American soil' in pre-taped segment
> Primetime Emmys 2011: Jane Lynch confronts 'Glee' alter ego Sue Sylvester
> Alec Baldwin 'walks out of Emmys'
> Primetime Emmys 2011: The major winners