The Latics were 1-0 up just five minutes into the contest thanks to Shaun Maloney's penalty after Robert Huth had handled in the box, but they then conceded a spot-kick in similar circumstances five minutes before the break, Maynor Figueroa being penalised and Jon Walters converting.
Franco Di Santo's goal on the break five minutes into the second half put the hosts back in front, but Crouch levelled in the 76th minute to ensure the Potters' third draw from three league matches so far this season.
Wigan will have gone into the game full of confidence off the back of two victories over the past week, last Saturday's 2-0 league win at Southampton and a 4-1 Capital One Cup triumph at Nottingham Forest on Tuesday.
They also had a decent record against Stoke, losing only one of the eight Premier League meetings between the two teams, and it did not take long for Roberto Martinez's side to get on top once this afternoon's contest got under way.
The hosts exerted some early pressure and after James McCarthy had seen his shot strike Huth's hand in the area, referee Martin Atkinson awarded a spot-kick which Maloney comfortably tucked away, sending Asmir Begovic the wrong way.
Wigan appealed for another penalty just before the quarter-hour mark, with Di Santo appearing to be sandwiched by Ryan Shawcross and Andy Wilkinson, but Atkinson ruled the infringement to be on the part of the Latics player.
Martinez's men kept pressing with crosses into the box and the ball just not quite falling for Arouna Kone, but they were disrupted by an enforced change in the 28th minute as the injured Jean Beausejour was replaced by David Jones.
Stoke issued a warning soon after, with Geoff Cameron cracking one wide from distance, and the visitors then made an early substitution of their own, with transfer deadline day signing Charlie Adam coming on for his debut in place of Wilkinson.
The Potters were finding some rhythm and after an Adam free-kick had caused a goalmouth scramble which Wigan survived, the Staffordshire outfit drew level.
Again it came from a handball in the area, Figueroa the culprit as Crouch tried to get past him, and Walters stepped up to slot the resulting penalty past Ali Al Habsi.
Stoke finished the half strongly with Marc Wilson's volley deflected against the bar, but Wigan began the second period as they had the opening one, netting early on to restore their lead.
A counter-attack move saw Kone find himself through on goal and with red and white shirts advancing he laid the ball off to Di Santo, who fired in.
The Potters responded with Michael Kightly drilling in to Al Habsi's arms, but Wigan continued to attack and after Kone had just failed to find the right pass following a run into the box, Emmerson Boyce struck an effort wide.
Having weathered the storm, Stoke hit back and Walters met a long ball at the back post but could not keep his shot down.
Crouch then provided the equaliser with 14 minutes remaining, leaping to nod in Walters' cross.
The momentum was fully with the Potters again and after Al Habsi produced a save to deny substitute Cameron Jerome, he pulled off a superb one to keep the ball out when Adam's free-kick deflected off Gary Caldwell.
It was very much end-to-end stuff in the closing stages and the home fans cried out for another penalty as Shawcross tackled Wigan substitute Ryo Miyaichi in the box, but Atkinson rightly waved play on before blowing the full-time whistle to confirm the points were shared.