Wolvaardt retired on 101 off 148 deliveries (13 fours) having been involved in fruitful top-order partnerships with Lara Goodall (51) and Andrie Steyn (31) to help guide the Proteas to 301 all out after 80 overs. Captain Sune Luus made 48.
England A spinner Sarah Glenn took 5-47 in her 20 overs.
Marizanne Kapp, Anneke Bosch and Tumi Sekhukhune then each picked up a wicket as England finished the day on 54-3 after 17.5 overs, still trailing by 247 runs.
The Proteas will face England in a one-off Test in Taunton from 27-30 June.
