Danny Williams had opened the scoring early in the second half of the Championship match, but the visitors were denied maximum reward from their trip to South Yorkshire.
With the clock counting down, Reading looked set to take all three points after largely keeping the hosts at bay, until Sougou struck following a lapse from goalkeeper Jonathan Bond, who failed to deal effectively with a ball pumped into the area.
Wednesday head coach Carlos Carvalhal handed a debut in goal to summer recruit Lewis Price, who replaced the injured Keiren Westwood.
The hosts made a positive start to the game and Marco Matias tried a volley early on which took a deflection wide.
Reading’s Oliver Norwood took a long-range free-kick which cleared the bar. The visitors soon posed another attacking threat when Chris Gunter put an effort over.
Wednesday were forced to make a change in the late stages of the first half when skipper Glenn Loovens limped off and was replaced by Vincent Sasso.
As the visitors continued to press in the final third, Williams fired in a shot which took a deflection wide.
Wednesday survived a scare soon after the re-start when Price failed to hold on to Orlando Sa’s firm drive and Hal Robson-Kanu – under pressure from Tom Lees – failed to hit the target from the rebound.
The respite was only temporary, however, as Williams put Reading in front in the 49th minute, firing past Price from inside the area after receiving the ball from the lively Sa.
Price was called into action to save Norwood’s free-kick as Reading went in search for a second goal.
Sougou, brought on in the 57th minute, found Matias in a promising position with a good ball from the right, but the forward failed to make a good connection and Bond gathered the ball easily.
It looked like being a fruitless night for the Owls, who failed to find the potency in attack that saw them win their first two home fixtures of the season, scoring six goals in the process.
But Sougou ensured that Wednesday’s unbeaten record at Hillsborough remained intact when he pounced in the area after Bond spilled a deep cross from Rhoys Wiggins and found the net with a first-time shot.
The goal provided much relief for Wednesday, who had failed to force Bond into making a serious save, ensuring their fans went home reasonably happy.