The ruling African National Congress had demanded Mbeki step down because of his rivalry with party chief Jacob Zuma, and Mbeki said Sunday he would resign.
Tutu, a Nobel laureate, conceded that Mbeki had made enemies due to "his intolerance of challenges and dissent."
"Those enemies have got their revenge, and are gloating as they rub his nose in the mud," Tutu said. "There is nothing principled about that. It is good old fashioned tit for tat."
"The way of retribution leads to a banana republic," he said.
Tutu voiced concern that Zuma still faces corruption allegations, and said they would remain until Zuma was tried for allegedly accepting bribes in a huge arms scandal that erupted nearly a decade ago.
Tutu had strained relations with Mbeki after criticizing his government for doing too little to alleviate poverty.
He also has upset Zuma supporters by saying Zuma is not suitable to become South African president after being accused of both rape and corruption.