Michael Olise calmly slotted in the resultant spot-kick to put the Royals in front.
After a poor run of four defeats in five matches, Reading had arrested the slide with successive 1-0 wins over Rotherham and Blackburn.
Darren Moore, appointed Wednesday manager on Monday after leaving League One Doncaster, oversaw a 2-1 home defeat to 10-man Rotherham in his first game in charge in midweek and his side had lost five straight games going into the Madejski Stadium clash.
He sustained a shoulder injury when taking part in a training session in midweek and wore a sling on his left arm while standing in the technical area.
Reading went in front on the half-hour. Puscas raced clear of the visitors' poor defensive cover and was clearly brought down by Borner, with the German centre-back picking up Wednesday's seventh red card of the season.
It was also the fourth successive league fixture against Reading in which the South Yorkshire team had had a player dismissed.
Joao was relieved of his usual penalty-taking duties – having missed three of his seven attempts this term, including in the 1-0 defeat at Wycombe last month.
Olise stepped up to confidently to beat Joe Wildsmith from the spot for his fifth goal of the campaign.
Wednesday survived until the break without further damage but Joao twice went close to stretching the home side's lead early in the second period.
First, he flicked on an Olise corner to the near post only for the ball to bounce off the bar to safety and he then volleyed wildly wide from an excellent Olise cross.
Wednesday offered little going forward, with Reading maintaining their high tempo and Tom Holmes shaving a post from 20 yards.
But their pressure paid off midway through the half when Joao expertly finished from inside the box.
Yiadom then settled the issue in the 88th minute, cleanly drilling home his first goal of the season.