Critics accuse Mbeki of using state institutions to protect allies and stifle opponents, allegations he denies.
Mbeki had stood by Selebi despite repeated calls by the opposition for his dismissal, saying he could only act against the police chief when a clear case against him was established.
"That is the only time when we say 'ok, if you think you have a case to pursue, that is it, please pursue,' and the president acts against the person," Mbeki's lawyer, Mojanku Gumbi, told a news conference.
Mbeki placed Selebi on extended leave on Saturday, a day after prosecutors said they would charge the police chief with corruption, fraud, money laundering and racketeering. Selebi denies any wrongdoing.
A copy of Selebi's indictment, made available to the media by the National Prosecuting Authority (NPA), includes receiving payments from his friend Glen Agliotti, a convicted drug smuggler accused of playing a role in the 2005 murder of a South African mining magnate.
Gumbi said Mbeki acted immediately after the NPA said it was ready to charge Selebi.
"The president immediately activated the government machinery ... and acted on the matter," she said.
Selebi resigned as president of Interpol as he fights the corruption allegations, the world police organisation said on Sunday.