Newcastle's defeat means leaders Brighton & Hove Albion, who had beaten Queens Park Rangers 2-1 on Friday, remain two points clear at the top of England's second-tier league with five games remaining.
Both the top two, though, remain overwhelming favourites for automatic promotion to the Premier League.
Rafael Benitez's Newcastle almost opened the scoring in stunning fashion when Jonjo Shelvey hit the bar from the halfway line at the end of a breathless first half.
Against the run of play, Tom Lees then opened the scoring for Wednesday with a powerful header after the break before Steven Fletcher doubled the lead with an outstanding header.
Read the full article on eurosport.co.uk: Newcastle miss chance to go back top with Wednesday defeat