Habana, who has 47 tries in 83 Tests, and the other five players would have been awarded national contracts for 2013 if not for their decisions to move to Europe or Japan, the South African Rugby Union said.
Flyhalf Morne Steyn, fullback Zane Kirchner, wing JP Pietersen and locks Andries Bekker and Juandre Kruger were also left off the 15-player list as they're set to leave South Africa toward the end of the season. SARU said a further five national contracts were still available and would be awarded later.
SARU chief executive Jurie Roux recognised the trend which has been exacerbated by the weakening of the South African currency and has seen front-line Springboks - and not only fringe players - take up big-money contracts overseas.
"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," Roux said.
Habana has signed for big-spending Toulon of France and will move at the end of the Super Rugby season, although the prolific wing has said he will still be available for the Springboks. However, there are obvious logistical difficulties in having senior national team members playing in the European or Japanese seasons.
"Losing experienced players to overseas teams is not ideal, but it's their right to further their careers abroad," coach Meyer said.
In response, SARU named a reasonably young 15-man group of centrally contracted players with an average age of 26.
Captain Jean de Villiers, flyhalf Pat Lambie, 21-year-old lock Eben Etzebeth and front-row regulars Tendai Mtawarira, Bismarck du Plessis and Jannie du Plessis all were given contracts, as were loose forwards Willem Alberts, Marcell Coetzee, Pierre Spies and Duane Vermeulen.
Schalk Burger was not on the list after he struggled with knee and calf injuries and then recently contracted bacterial meningitis. The former IRB world player of the year hasn't played for over a year.
Habana ended 2012 in top form and was voted South Africa's Player of the Year for the third time despite a late-season injury.
Fellow wing Pietersen and Kirchner were first choices in their positions, while Bekker and Kruger were South Africa's top two No 5 locks last season. Although Steyn lost his starting place, he was expected to remain important for the Springboks this year after the loss to injury of young No. 10 Johan Goosen.
Pietersen is set to play in Japan and may not be available for the Boks' Rugby Championship campaign against world champions New Zealand, Australia and Argentina over the next two seasons. Steyn, Kirchner and Kruger will also likely miss time in the national jersey. Towering second-rower Bekker was left out of Meyer's first Springbok squad of the season altogether, suggesting he won't be considered at all while he plays in Japan.
Starting scrumhalf Ruan Pienaar and openside flank Francois Louw already play overseas.
Springbok contract group:
Willem Alberts - Sharks
Marcell Coetzee - Sharks
Juan de Jongh - Western Province
Jean de Villiers - Western Province
Bismarck du Plessis - Sharks
Jannie du Plessis - Sharks
Eben Etzebeth - Western Province
Francois Hougaard - Blue Bulls
Pat Lambie - Sharks
Tendai Mtawarira - Sharks
Pierre Spies - Blue Bulls
Frans Steyn - Sharks
Adriaan Strauss - Free State Cheetahs
Flip van der Merwe - Blue Bulls
Duane Vermeulen - Western Province