Lightning-quick full-back Ryan Sessegnon and Aleksandar Mitrovic combined nine minutes from time to pull Fulham to within two points of second-placed Cardiff as they extended their unbeaten run to 20 matches.
Sessegnon, who is being monitored by a host of Premier League clubs, was released down the left as he had been frequently throughout the game but this time his cross was pinpoint and Mitrovic - on loan from Newcastle - made it nine goals in nine games from six yards out.
It was the least Fulham deserved from a controlled performance. They could have had more were it not for the performance of Owls goalkeeper Joe Wildsmith who saved from Sheyi Ojo, Stefan Johansen and Neeskens Kebano. Sessegnon also clipped the top of the cross bar with a looping header.
Wednesday came into the game on the back of an encouraging run of three wins and a draw from their previous four games which had seen them allay any fears their injury-hit campaign would end in a battle against relegation.
But apart from some neat build-up play they could not create any clear-cut chances.
Tom Lees had described the fixture as a god baramoter of where the Owls are and on this evidence they remain some way off challenging at the top end of the Championship.
They did lose Barry Bannan to injury after 30 minutes but Owls fans were heartened to see a 15-minute cameo by Fernando Forestieri, who has missed much of the season through injury.
Forestieri could have equalised in stoppage time but blazed over.
Wednesday manager Jos Luhukay said: “From the result it’s disappointing, but I think in the first half we’ve come to some situations that we’ve created some chances, although coming to the last ball it was not always in the right direction.
“In the second half, no control, we were only defending, and Fulham were a lot stronger than we were, they had more chances aside from their goal, they could have scored three or four times.
“(Goalkeeper) Joe Wildsmith was the best player in our team, that says enough about our team. We lost the game against a very strong team. I have analysed Fulham, they are very intense and in the second half I see why this team is challenging for the top two positions.
“In the second half we were losing the ball and Fulham were pressing us directly and we could not come out. It was also not our strikers’ day, they couldn’t get on the ball and when they did it was not on dangerous areas.
“It was just working, fighting, defending and when we did have the ball we couldn’t play football.”