Three-time champion Becker was jailed for two-and-a-half years back in April after being found guilty of concealing £2.5million of assets to avoid paying money he owed after his bankruptcy.
The six-time grand slam winner has been a regular on the BBC’s coverage of the tournament for many years and was present alongside McEnroe and Barker last year.
“Boris, we love you. We miss you, man,” McEnroe said during Monday’s broadcast before Barker added: “We do indeed.”
Viewers criticised the pair for their comments and for using the BBC’s platform to “send greetings” to a “convicted criminal”.
They come just a week after McEnroe expressed support for his former colleague and revealed plans to visit him in prison.
“Boris is a friend of mine. This is just horrible. I want to see him if I possibly can and if he’s willing to see people,” he said.
“I just feel terrible. He’s one of the great players that has ever played the game, and I know it meant a lot to Boris. He’s been going through a lot for a long time.”
Becker is currently serving his sentence at HMP Huntercombe in Oxfordshire but could be deported as early as next year.