Philander had figures of five for seven from six overs as New Zealand failed to cope with good fast bowling on a well-grassed pitch after winning the toss. Morne Morkel took three for 14 and Dale Steyn two for 18.
Although the pitch gave some help to the fast bowlers, South Africa's free-scoring reply showed there were no devils in the surface.
Captain Graeme Smith was leg before wicket to Doug Bracewell for one to become the eleventh man dismissed before lunch, but Hashim Amla and Alviro Petersen shared a second wicket stand of 107.
Amla hurried to a half-century off 55 balls before he walked across his stumps and was leg before wicket to James Franklin. New Zealand, fielding a team hit by injuries and controversy, contributed to their collapse with uncertain foot movement against Philander, who stuck to his tried and tested method of bowling in a tight channel at a lively pace.