The South African Rugby Union confirmed on Wednesday that senior internationals Habana, Morne Steyn, JP Pietersen, Andries Bekker, Juandre Kruger and Zane Kirchner had not been given contract renewals for 2013.
"All six of these players were going to receive contracts, but the fact that they have indicated that they have signed with overseas clubs or are planning to do so, has ruled them out of the reckoning," SARU chief executive officer Jurie Roux said.
Springboks coach Hanke Meyer admitted losing the players abroad was not ideal, but welcomed the chance for the likes of rising stars Eben Etzebeth, Marcell Coetzee, Juan de Jongh and Pat Lambie to be included on the 15-man list.
"I'm very excited about the contract group. Most of these players showed last year they have what it takes to play for the Springboks and they can only get more experienced and improve further," he said.
"Losing experienced players to overseas teams is not ideal, but it's their right to further their careers abroad."
Habana, who has scored 47 tries in 83 Tests, is set to move to Toulon at the end of the Super 15 season but has previously stated his intention to remain available for national duty.
Steyn and Kruger will follow him to France while Pietersen and Bekker are set to take up lucrative deals in Japan.
Kirchner will join established Springboks Ruan Pienaar and Francois Louw in Great Britain to underline the player drain caused in part by South Africa's falling currency.
"We've kept as many of our top players in South Africa as we could by awarding them national contracts, despite the powerful lure of the pound, euro and yen," said Roux, who revealed a further five contracts were still up for grabs.
"We worked hard with the Springbok Management and Sarpa (South African Rugby Players Association) to ensure the best possible deal is placed on the table for the players.
"Last year provided Heyneke Meyer with an ideal opportunity to see what is needed in the Test arena, and by contracting this group of players, we have secured a core group for 2013.
"The average age of the contracted group is not very high for Test rugby, which bodes well for the future."
Contracted players: Willem Alberts, Marcell Coetzee, Juan de Jongh, Jean de Villiers, Bismarck du Plessis, Jannie du Plessis, Eben Etzebeth, Francois Hougaard, Pat Lambie, Tendai Mtawarira, Pierre Spies, Frans Steyn, Adriaan Strauss, Flip van der Merwe, Duane Vermeulen.