He voted shortly after 2 pm at the library building in the University of Limpopo, outside Polokwane, where the ANC is holding its 52nd national conference.
Trailed by a bodyguard holding a large red umbrella to shield him from a chilly drizzle, Mbeki smiled and waved to supporters from the Eastern Cape, one of the four provinces that has backed him in the battle against his rival for the presidency, Jacob Zuma.
Zuma himself voted shortly after polling opened at 9am on Tuesday.
Many observers are predicting a win for Zuma, and his supporters were on Tuesday convinced that they smelled victory.
"We have done it, as we have been saying all along. Zuma is an unstoppable tsunami," said an ebullient Jim Mkandawire after he had voted.
"I love Mbeki but believe that politics in the ANC is like a relay. He has to hand over the stick to another person".
Gauteng delegate Jane Mathe came out of the voting station loudly singing the song "Dedela abanye", Xhosa for "give others a chance".
"I'm happy that the long wait is over. This is the last kicks of a dying horse", she said.
Mbeki supporters were quiet with most of them refusing to talk to the media after casting their votes.
Voting for the presidency and the other top five leadership positions in the party was supposed to start at 6am, but was delayed three hours.
Party spokesman Steyn Speed said this was because nominations had begun so late on Monday night and ballot papers for the 3 900 voting delegates still had to be printed.
About 40 election officials worked through the night to complete this, and to go through the voter's roll after the credentials of the voters had been adopted.
In addition, there were also delays due to computer problems, said Bertha Gxowa, ANC electoral commission chairwoman.
The votes are to be counted manually amid fears of vote rigging.
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