After Dan Armstrong fired in Wolves’ opener following Connor Levingston’s parried shot, Ngoy controlled Eddy Lecygne’s pass before scoring the equaliser.
Neither side could find a winner after the break, meaning Stoke earned a fourth consecutive 1-1 Premier League 2 draw and moved up to 10th.
Wolves are third, behind second-placed Fulham on goal difference and three points above sixth-placed Aston Villa. Teams ranked second to fifth will compete in the play-offs for promotion to Division 1.
Wolves next face Norwich City at New Bucks Head on Monday 10 April, while Stoke visit Brighton on the same night.