Storey, who was recalled to the side in place of Dominic Iorfa for the trip to the University of Bolton stadium, poked the ball over the line from a second-half corner to give the visitors the lead in front of more than 5,000 ecstatic travelling fans.
But defender MJ Williams fired home from a corner kick at the other end in added time to deny Darren Moore’s side all three points in Lancashire.
Wednesday remain fifth in League One, level on points with the two sides below them.
Scroll down for our player ratings.
1. bolton v owls 6(goal).JPG
Jordan Storey pokes the ball home for Sheffield Wednesday. Photo: Steve Ellis
2. Bailey Peacock-Farrell - 6
Stopped a goal-bound strike from close range in his first activity of the afternoon, which was otherwise relatively quiet. Little chance with the goal, a bitter pill to swallow. Photo: Steve Ellis
3. Harlee Dean - 7
Got stuck in, as you would expect, and grabbed the assist for the opening goal with a towering header. Generally looked solid in both boxes. Photo: SWFC
4. Jordan Storey - 6
Poked the ball over the line for the opening goal, atoning for a first-half error which saw him give the ball to Bolton for a goalscoring chance. Photo: Steve Ellis