The 31-year-old, who has earned 72 caps since his debut in 2002, takes charge on a temporary basis and will lead the team for the three-match Test series against England which starts in Durban on Saturday.
De Villiers, the Stormers skipper, succeeds veteran hooker John Smit after his retirement from international rugby last year.
Meyer has defended his selection after he stuck with a tried and tested crop of players in his team selection.
While many of his decisions were expected, he surprised fans by including only three Stormers players in his group for the first series of his tenure.
The Stormers cemented their place at the top of the South Africa conference in the Super Rugby competition when they beat the Bulls 19-14 at Loftus Versfeld on Saturday.
“I don’t count which guys are in which teams. I just pick the guys I believe are the best,” Meyer said after the brutal north-south derby in the capital.
The right team
“There are a lot of their great players injured, like Duane Vermeulen, who is a great player, Schalk Burger and Andries Bekker, who is also not around.
“If I pick a team I need to pick the team that I believe is the right one.”
Meyer said the Stormers had a number of talented youngsters coming through the ranks and it was only a matter of time before more players in the side earned their Springbok colours.
He added that the match between the Bulls and the Stormers was a window into the kind of game plan the Springboks would adopt.
“I think it was a great spectacle in typical Test match rugby [style] and that is how I want the Boks to play,” Meyer said.
“Obviously you want to score tries and get the people on their feet but for me it is all about playing tactically well and playing winning rugby.
“England are a tough team and they’ve been together for quite some time so it’s not going to be easy.
“We need to play a type of rugby typical to South African strengths.”
A direct, physical approach also fitted into the Bok mentor’s fondness for big, strong, athletic players, which did not bode well for the likes of Stormers backline players Gio Aplon and Juan de Jongh, who did not get a call-up, despite their skill and individual attacking brilliance.
Another notable omission was that of scrumhalf Fourie du Preez, who was reported to be the favoured candidate to captain the side.
“I’ve had a few meetings with him [Du Preez] and I discussed the situation of him coming back to play,” Meyer said.
“He always believes that the team comes first and when we had a conversation he said he wasn’t 100% sure if he could do his best because he hasn’t played for two-and-a-half months.”
Meyer complimented Du Preez for his honesty and opting to step aside to give new blood a chance to take ownership of the number nine jersey.
“I’ve said from the start I want these guys to go in there and know they are 100% right and each guy tries to give 100% for his country,” he said.
South Africa squad
Zane Kirchner (Bulls), JP Pietersen (Sharks), JJ Engelbrecht (Bulls), Jean de Villiers (Stormers), Wynand Olivier (Bulls), Francois Steyn (Racing Metro/FRA), Bryan Habana (Stormers), Lwazi Mvovo (Sharks), Bjorn Basson (Bulls), Morne Steyn (Bulls), Patrick Lambie (Sharks), Elton Jantjies (Lions), Francois Hougaard (Bulls), Jano Vermaak (Bulls), Ruan Pienaar (Ulster/IRL)
Tendai Mtawarira (Sharks), Coenie Oosthuizen (Central Cheetahs), Bismarck du Plessis (Sharks), Chiliboy Ralepelle (Bulls), Adriaan Strauss (Cheetahs), Jannie du Plessis (Sharks), Werner Kruger (Bulls), Eben Etzebeth (Stormers), Flip van der Merwe (Bulls), Franco van der Merwe (Lions), Juandre Kruger (Bulls), Marcell Coetzee (Sharks), Willem Alberts (Sharks), Pierre Spies (Bulls), Ryan Kankowski (Sharks), Keegan Daniel (Sharks), Jacques Potgieter (Bulls) – Sapa