The Proteas captain struck a majestic 169 off 143 balls to help her side to a total of 319-7 before Marizanne Kapp then took career-best figures of 5-20 as England were bowled out for 194.
After being put in to bat, Proteas opening pair of Wolvaardt and Tazmin Brits put on on a partnership of 116.
It would have settled any nerves in the dressing room after they were bowled out for just 69 against England in their opening match of the tournament.
Brits lost her wicket in the 23rd over, bowled by Lauren Bell, for 45 to trigger a mini-collapse that saw the Proteas lose three wickets for just three runs.
Anneke Bosch lasted three balls before being bowled by Sophie Ecclestone before Sune Luus was sent packing by England skipper Nat Sciver-Brunt to leave the Proteas 119-3.
Wolvaardt then combined with Kapp for a crucial 72-run partnership with Kapp aggressively making her way to 42 off 33 balls.
Kapp (42) then skied Ecclestone going for another big shot and Proteas lost another three wickets in quick time to leave them on 202-6.
All the while Wolvaardt was going on her merry way at the other end and brought up her century off 115 balls before cutting loose in the final 10 overs.
The Proteas captain slammed four sixes and found a good partner in Chloe Tryon as the duo put on 89 from just 47 deliveries to take the side over the 300-run mark.
Wolvaardt was dismissed with two overs remaining but walked off to a standing ovation with every one of the England players coming to her to offer a handshake.
Tryon remained unbeaten 33 while Nadine de Klerk was 11 not out as the Proteas would have felt might pleased with the total.
Kapp then rattled England with two wickets in the first over of the run-chase before Ayabonga Khaka got another scalp in the second over to with the score reading 1-3.
Sciver-Brunt (64) and Alice Capsey (50) put on 107 for the fourth wicket but the Proteas were not to be denied as Kapp returned to in the middle overs to dismiss the England skipper.
The Proteas allrounder then cleaned up Charlie Dean and Sophia Dunkley to complete her second five-wicket haul in her ODI career.
West Indies strengthened their position in Group C of the T20 World Cup with a 30-run victory over England in Mumbai, as a dominant spin performance dismantled Harry Brook's side after a bright start to their chase.
Kayla Reyneke enjoyed a dream debut with bat and ball, including hitting the winning runs off the final delivery of the game, as the Proteas Women beat Pakistan by five wickets in the first T20I in Potchefstroom.
England head coach Brendon McCullum insists Harry Brook is a "strong leader" and the right man lead the white-ball teams despite plenty of off-field controversies in recent months.
England defended a target of 129 to beat Sri Lanka by 12 runs and complete 3-0 series clean sweep in Pallekele in what will be seen good preparation ahead of the T20 World Cup.
