Boro, who spurned a host of opportunities, did things the hard way after trailing on the half-hour after Ross Wallace put the hosts ahead.
But Howson’s long-ranger in the 71st-minute proved too hot to handle for Owls keeper Joe Wildsmith, who had made a fine penalty save to deny Grant Leadbitter moments earlier, as the Teessiders restored parity.
And their reward for a second half in which they were dominant, came seven minutes from time from an unlikely source when Shotton, making just his second league start for Boro and first since September 30 powerfully headed in a corner from the impressive Stewart Downing.
Wednesday, whose winless streak extended to seven matches, could have few complaints at the outcome, even taking their raft of injuries into account.
Chants of ‘We Want Carlos Out’ arrived from disgruntled sections of Wednesdayites towards the end, with boos arriving at the final whistle, with fans justifyably feeling short-changed at the hosts’ poor second half showing, with the Owls languishing in a hugely disappointing 15th spot.
For Boro, there was encouragement following woeful away performances at Millwall, Bristol City and Leeds United, with their visiting contingent given something to cheer about, belatedly.
A number of striking selection calls caught the eye ahead of the game, most notably the promotion of Frederico Venancio and Atdhe Nuhiu to the Owls’ starting line-up.
Portuguese defender Venancio was handed a Wednesday debut in place of the injured Glenn Loovens, while Nuhiu - who has previously tormented Boro en route to scoring four goals against the Teessiders earlier on in his Owls career - lined up for his first start since last New Year’s Eve.
Sam Hutchinson, handed the captain’s armband, was given his first league start since August 12, while it was also a noteworthy afternoon for visiting centre-half Ryan Shotton, named in the starting XI just for the second time in his Boro career.
An entertaining first half saw Wednesday head into the interval with a precious lead, courtesy of Wallace’s neat opener, while Boro - despite some eye-catching approach play orchestrated chiefly by Stewart Downing - were left to rue a lack of a killer edge in front of goal.
The Teessiders spurned several excellent opportunities, none moreso than when Patrick Bamford planted a weak header wide with all the goal to aim after being left with the freedom of the area following Cyrus Christie’s centre.
The gravity of that miss was exposed when a quality move involving Boro old boy Adam Reach and Gary Hooper unhinged Boro and with their defence stretched, Wallace coolly fired home low past Darren Randolph on the half-hour.
Despite the set-back, Boro produced a strong spell before the break, but were wasteful in front of goal.
First, Jonny Howson hooked over from close range before an incisive move dissected Wednesday after Martin Braithwaite latched onto Downing’s astute defence-splitting pass.
After rounding Joe Wildsmith, the Dane cut the ball back into the danger area with the ball breaking for Britt Assombalonga, whose close-range shot was blocked by Daniel Pudil.
Soon after, Boro’s £15m man steered an effort wide of goal after a neat pass from Howson as the chances started to stack up for the visitors - with the half ending with a low drive from Liam Palmer stinging the palms of Randolph.
After benefitting from the visitors’ profligacy in front of goal in the first half, Wednesday could at least reflecting upon a positive scoreline, but they failed to make the most of that situation and produced an abysmal second-half.
Boro pressed with Braithwaite spurning a golden chance after great work from Bamford and Fabio before a bnudled goal from Assombalonga was ruled out for offside.
Wednesday finally cracked when Venancio was penalised for a foul on Bamford in the box, with Peter Bankes pointing to the spot, only for Wildsmith to guess right and make an outstanding save to deny Leadbitter.
But it proved a bittersweet moment, with the keeper flapping at a long-range strike from Howson, which he only helped into the net.
Boro pushed for the winner and after a rare home chance saw Reach head straight at Randolph, the winner arrived when Shotton headed in Downing’s corner.
Sheffield Wednesday: Wildsmith; Palmer, Venancio, van Aken, Pudil (Joao 81); Wallace (Butterfield 65), Jones, Hutchinson, Reach; Hooper, Nuhiu. Substitutes unused: Dawson, Rhodes, Joao, Matias, A Baker, Abdi.
Middlesbrough: Randolph; Christie, Shotton, Gibson, Fabio; Leadbitter, Howson; Braithwaite (Johnson 64), Bamford (Gestede 83), Downing (Tavernier 90); Assombalonga. Substitutes unused: Konstantopoulos, Friend, Ayala, Fletcher.
Referee: P Bankes (Merseyside).