Despite averaging 21 and making 24 dismissals in nine tests since his debut against South Africa in New Zealand last year, van Wyk lost his place to another South African-born player, B.J. Watling.
Watling, who has played just one test for New Zealand, was favored by selectors for his superior batting ability. He has been sidelined with a hip injury since his wicketkeeping debut for New Zealand last summer.
Veteran batsman Peter Fulton has been recalled to the New Zealand squad after a three-year absence and will vie with Australian-born Dean Brownlie to replace former captain Ross Taylor in the batting lineup.
Taylor declared himself unavailable for the tour on Friday after being fired as captain. Brendon McCullum will now captain New Zealand in all forms of the game, beginning with its two tests, three one-dayers and Twenty20 internationals in South Africa.
The test squad named on Friday includes off-spinner Bruce Martin who will make his international debut aged 32 and after a 13-year first class career. Martin replaces injured left-armer Daniel Vettori and legspinner Todd Astle, who played in New Zealand's most recent test series in Sri Lanka.
"We don't require a leg-spin option in South African conditions so have left out Todd Astle, but he is very much part of our thinking for the future," New Zealand coach Mike Hesson said. "Bruce Martin is a specialist spinner who can bowl a lot of overs and he deserves an opportunity after showing good recent form."
The New Zealand Twenty20 squad includes a number of newcomers to international cricket: Corey Anderson, Jimmy Neesham, Colin Munro, Derek de Boorder and Mitchell McClenaghan.
Hesson said all five had shown "considerable promise" in domestic matches and deserved a chance at international level.
"We believe the squad has a good blend of experience and young talented players who we are sure are ready for the challenges ahead," he said.
New Zealand Squads:
Test squad: Brendon McCullum (captain), Trent Boult, Doug Bracewell, Dean Brownlie, Daniel Flynn, James Franklin, Peter Fulton, Martin Guptill, Chris Martin, Bruce Martin, Jeetan Patel, Kane Williamson, Tim Southee, Neil Wagner, B.J. Watling.
Twenty20 squad: Brendon McCullum (captain), Corey Anderson, Trent Boult, Doug Bracewell, Derek de Boorder, James Franklin, Peter Fulton, Martin Guptill, Ronnie Hira, Nathan McCullum, Mitchell McClenaghan, Adam Milne, Colin Munro, Jimmy Neesham, Rob Nicol.
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