Heskey lost his composure after not winning a free-kick and appeared to barge into the official. But he escaped with a yellow card and was substituted at half-time.
A share of the spoils kept Wigan's survival hopes alive ahead of next week's crunch meeting with West Ham.
Charles N'Zogbia gave Wigan a 10th-minute lead. Victor Moses made a purposeful run before slipping the ball into N'Zogbia, whose low shot flew past Brad Friedel into the corner of the net.
But after 17 minutes, Ashley Young brought Villa level. The England winger was brought down in a central position 20 yards out by Ben Watson. Young played a short free-kick to Stiliyan Petrov before receiving the ball back and curling a low shot wide of the defensive wall into the corner of the net.
Heskey was shown a yellow card after 33 minutes after he appeared to barge into referee Jones. He was clearly unhappy at not being given a free-kick after a tussle with Gary Caldwell. Skipper Petrov was spoken to by Jones about the behaviour of the striker and caretaker manager Gary McAllister replaced him with Marc Albrighton for the second period.
Source: PA
Source: PA