Madine ended a four-month goal drought to set the Owls on their way to a victory that keeps them above the drop zone, though Reda Johnson's header proved decisive after Jacob Mellis nicked an injury-time consolation.
"Gary had a good season last year and he scored a lot of goals," said Jones, whose side are still just a point clear of danger after rivals Wolves and Peterborough also won.
"He has struggled to adapt at this level but he has worked at it and worked it. There has been a lot said about a falling out. There has never been any problems.
"Strikers are a commodity that everyone wants if they can score goals. It's nice for him to get his goal.
"If I didn't feel he could score goals he wouldn't be here. We will keep working with him."
Wednesday were second best until Madine's opener, but Jones felt his side were worthy winners in the end.
"The second half we took it to them and thoroughly deserved the win in the end," he added.
"It was all about getting the three points for us. We got in behind them a couple of times in the second half and could have won by more."