Three points in their predicament at the foot of the table may be a drop in the ocean of gains they will need to survive but Danny Wilson's side deserved their win, much as injury-hit Middlesbrough's second-half improvement had them in a flap at times.
Wednesday's occasional sharpness made a nonsense of their woeful record. In the first half in particular, Middlesbrough, a team prone to blow hot and cold, were outplayed as the class of Wim Jonk stood out in midfield and Niclas Alexandersson tormented Curtis Fleming on the right flank.
Even before Atherton headed them in front, neatly directing Alexandersson's cross past Mark Schwarzer, Danny Wilson's team had created several dangerous moments, going closest through the heads of Andy Booth and Danny Sonner.
After Atherton's goal, penalty claims were mysteriously waved away after Mark McKeever, the 21-year-old making his Premiership debut, was clearly fouled by Robbie Stockdale. But more followed from the blue and white stripes. Andy Hinchcliffe's free-kick required Schwarzer to save, then Alexandersson saw his shot deflected for a corner following a one-two with Gilles de Bilde.
Only Juninho, a bundle of energy as ever, seemed to have it in him to spark Boro and it was only when Carlos Marinelli, their 17-year-old Argentinian forward, came on at half-time, that Bryan Robson's team began to wake up. Marinelli, for whom Robson paid Boca Juniors pounds 1.5m, had been kept under wraps until yesterday. He may not been the "new Maradona" as some extravagant reports have suggested but he is not short of skill and first impressions are good.
With the youngster on board, the visitors tested Wednesday's nerve and Juninho ought to have scored after a Pavel Srnicek error. But Wednesday had chances to put the result beyond doubt when Jonk was inches away from converting an Alexandersson cross and De Bilde shot wide.
Goal: Atherton (28) 1-0.
Sheffield Wednesday (4-4-2): Srnicek; Nolan, Atherton, Walker, Hinchcliffe; Alexandersson, Sonner (Haslam, 65), Jonk, McKeever (Cresswell, 87); Booth, De Bilde. Substitutes not used: Pressman (gk), Sibon, Nicholson.
Middlesbrough (4-4-2): Schwarzer; Stockdale, Festa (Gavin, h-t), Vickers, Fleming; Stamp (Ricard, 75), Mustoe, Maddison, Juninho; Armstrong (Marinelli, h-t), Deane. Substitutes not used: Beresford (gk), Baker.
Referee: B Knight (Orpington).
Booked: Sheffield Wednesday: Jonk, Sonner, Booth, Cresswell. Middlesbrough: Festa, Stamp, Deane.
Man of the match: Alexandersson.
Attendance: 28,531.Reuse content