The Serbian, whose side continued in their hopeful march to the Championship playoffs, wore a sling throughout the match, which was turned by a 32nd-minute red card for Owls defender Julian Borner
Goals for Michael Olise, former Wednesday forward Lucas Joao and Andy Yiadom did the damage for the Royals.
Paunović’s side were frustrated by Tony Pulis’ Wednesday in a 1-1 Hillsborough draw back in December and he called back to that when discussing the nature of the win.
“Everyone can say whatever they want, but it’s not easy to play against a team who has 10 players and who know how to sit back, wait and build their momentum in the game,” he said. “They know how to look for their counter attacks and their set pieces and surprise you.
“That mind game is usually played every time this happened. Being one-nil up helps but we still had to do our homework and do our jobs, be patient, be consistent with our ballwork and recovery when we lost it. We could allow them to make counter attacks quickly.
“We defended our half very well and that helped us to build our momentum in the second half.”
On his injury, a badly injured collar bone, he said: “The most important thing is of course that the team won today. Unfortunately in one of our recovery sessions I got involved and fell awkwardly and injured my left shoulder.
“It’s pretty nasty, so I’ve spent the last couple of days dealing with that, but I’m well.”