Their eight-wicket win leaves the series 2-1 in West Indies' favour, with one match to play.
Wolvaardt, the 19-year-old, was back in the side after having played the first T20I of the series, and ended up guiding the chase with 54 not out off 57 balls, as South Africa brought up victory in 18.4 overs. Lee had made 54 off 38, with the openers putting on 89 runs in 12 overs.
Put in to bat, West Indies had made 135 for 3 at the Brian Lara Stadium in Tarouba. Natasha McLean batted through the innings, but made only 57 not out off 61 balls. Captain Stafanie Taylor too scored at less than a run a ball, but Deandra Dottin's 28 off 15 took them to 135 for 3.
Seamer Tumi Sekhukhune was the only wicket-taker for South Africa, with 2 for 27 in four overs, while Marizanne Kapp had economical figures of 4-0-13-0.
South Africa's chase was set on track by the openers, and even after Lee fell, Sune Luus joined Wolvaardt for a 45-run stand that took the visiting side to the brink of victory. Though Luus fell with two runs to get, captain Chloe Tryon - leading the side with Dane van Niekerk sitting out due to an ankle injury - came out to hit the winning runs.
For West Indies, Afy Fletcher took 1 for 12 in four overs, while Taylor had 1 for 16.