Djokovic said he will now make all the calls as he prepares for 2017.
"Thank U[sic]," Becker tweeted after news of his sacking was made public.
"We had the time of our life #teamdjokovic."
As recently as Monday, Becker had expressed uncertainty regarding his place in Djokovic's camp.
"I truly enjoyed the last three years; I had a blast," Becker told the Daily Mail this week.
"I was in my element and I will continue to be in my element in the future. No regrets, it was an unbelievable ride."
He also indicated there are "other issues" relating to Djokovic's recent dip in form and drop from the top ranking, but wouldn't be drawn on details.
"Look, I'm on the inside, I know everything, and I can't tell you," he said.
"I love my player and will protect him and will never say anything about that, so I will have to plead the fifth amendment."