The Portugal international looked visibly frustrated and unimpressed after coming off in the 58th minute of Saturday's Hillsborough encounter.
Joao shook his head in disbelief and threw some strapping around his leg on the ground before being replaced by home debutant Dominic Iorfa.
Bruce told The Star: "I think there was a bit of a mixed message there. We were hearing that he had hurt his knee. However, he had gone to the bench to say he wanted strapping around his knee.
"Lucas gave us 50 odd minutes.
"I don't give a jot when a player reacts (to coming off). I like it when they are not happy. Who is happy when they are pulled off? But I did genuinely think he had an injury."
It is the second match in a row where Joao has struggled to make an impact as a starter. The nine-goal star was also comfortably shackled against Rotherham United and taken off just before the hour mark in the South Yorkshire derby.
Bruce said: "I don't mind it when people are sulking when they get pulled off because it means something.
"He (Joao) is a good player is the kid. On his day, he is a handful for everybody. He knows what we expect and he will be fine."
Forward Fernando Forestieri will be pushing for a first-team recall when the Owls return to action against Brentford on Tuesday evening, having served a one-match suspension.
"The more options I have the better," said Bruce. "I thought we were just starting to see the best of Forestieri (before his Rotherham red card).
"When we get him up to speed, he is a good player."
It remains to be seen whether Morgan Fox (back), Jordan Thorniley (concussion) and George Boyd will be available for selection when Wednesday host the Bees.
Bruce said: "We had about 10 missing through illness and injury. Hopefully we will have a few recovered for Tuesday.
"We are playing a good side in Brentford and we will have to be at our best to beat team.”