Both sides were sluggish and lacked penetration in the opening 45 minutes, with neither goalkeeper being seriously tested until after the break.
Grant Leadbitter's clever free kick shook the hosts into life, helped moments later by the home fans' indignation at the sending-off of popular defender Daniel Ayala, rumoured to be on his way out of the club.
Alvaro Negredo and Marten de Roon scored to make the game safe but Boro could have had more, with de Roon pulled back when through on goal when an advantage should have been played, and Cristhian Stuani having a goal correctly ruled out for offside.
Much-maligned Stuani impresses in attack
Despite failing to put his name on the scoresheet, Uruguay international Stuani enjoyed one of his best Middlesbrough games in recent memory.
Despite his stunning double against Sunderland, his double-figure tally last season and the tap-in which sealed promotion from the Championship, Stuani has often cut a frustrating figure for fans at the Riverside.
Against Wednesday, he showed why Aitor Karanka views him as such an important member of the squad. Direct when he needed to be, sensible when he couldn't and tidy throughout, his excellent performance almost earned him a stunning goal right at the death.
Picking the ball up outside the penalty area, he showed some deft footwork to slalom between two defenders and looked to fire past the shaky-looking goalkeeper.
Joe Wildsmith saved his shot, but parried it into the path of De Roon, who slammed it into the top corner to round off the scoring. Had Stuani found the net, he would have had a richly deserved goal to cap a great performance.
De Roon enhances claim for fans' favourite
De Roon isn't an obvious candidate for fans' favourite in a stadium increasingly crying out for more attacking vigour, but the latest in a string of meaningful, attractive performances showed why he is beginning to pay back his hefty summer transfer fee.
Energetic running forwards and always keen to put in a challenge coming back, the Dutchman adds a useful dimension to Boro's at times sluggish midfield.
His goal against Wednesday took him to three for the season - more than Gaston Ramirez - and it was an impressive finish again, cannoned into the top-left from just inside the area.
At times, he is bypassed in games and his disciplinary record could be improved, but if he continues to improve then Middlesbrough have an excellent midfielder on their hands. Another creative addition in the transfer window, and he might just flourish.
Contrasting fortunes for Boro's forwards
It is fair to say that Jordan Rhodes might be one of the most unlucky men on Teesside. At 1-0, the game was perfectly set for him to come on and make an impact, with rumours of his potential exit from the club continuing to circle.
Wednesday were behind and would have to come out of their shells, leaving gaps at the back for the archetypal Championship penalty-box poacher, warming up on the touchline, to come on and steal a goal or two. 60 seconds later, he retook his place on the bench.
With Ayala dismissed, Karanka had to reorganise his defence and midfield. Negredo was left to complete the 90 minutes, and Rhodes was left ruing another missed opportunity to come on and impress.
Those who hold Rhodes up as the answer to Boro's goalscoring problems can have had no complaints about Negredo's performance today. He worked hard for his goal, and went close on more than one other occasion, but his hold-up play late in the game was the most impressive of all he did.
After working hard throughout in a game he might not have expected to start, the Spaniard's energy levels were constant and his dominant hold-up play allowed the rest of the Boro attack to dovetail around him and pull the Wednesday rearguard apart.