Deon Burton struck against the run of play at Ninian Park to deal a potentially deadly blow to Cardiff's hopes of forcing their way into the Coca-Cola Championship play-offs.
Burton bundled a Chris Brunt cross past home keeper Dave Forde at the second attempt in the 69th minute to continue the Bluebirds' slide out of the top six shake-up.
To make matters worse for Dave Jones' men, they ended the match with 10 men after Simon Walton was issued a deserved red card two minutes from time for a clattering challenge on Peter Gilbert.
Ironically Burton's winner came during Cardiff's best spell of the match, as they sought to build on Roger Johnson's equaliser in first-half injury time.
It looked like Wednesday would take a narrow lead into the interval after Leon Clarke took advantage of hesitation in the home defence to prod home the visitors' opener in the 39th minute.
Until that moment both sides had laboured for little reward, with Clarke hitting a low ninth-minute shot straight at Forde, and Joe Ledley striking Cardiff's best chance against the post.
Michael Chopra also came close to grabbing his 22nd goal of a profitable season when he swivelled on Peter Whittingham's 25th-minute cross before firing at Iain Turner from point-blank range.
Paul Parry hit a rising effort over the bar as the home side immediately pressed for an equaliser, which came in added time when Johnson firmly headed home from Kevin McNaughton's cross.
Johnson's goal clearly reinvigorated the home side who started the second half in crashing style and should have taken advantage of at least one of numerous chances to go ahead.
Warren Feeney headed narrowly wide moments after the restart before Walton drove a powerful shot into Turner's midriff and Chopra miscued an overhead kick in a dangerous position.
Increasingly finding themselves pinned back in their own half, Wednesday appeared incapable of doing anything to escape the waves of pressure until a dramatic turnaround in the 67th minute.
In their first foray over the half-way line for some time, Chris Brunt flung in a cross from the left and, after his initial header was parried by Forde, Burton bustled it home at the second attempt.
With the home fans becoming increasingly restless, Dave Jones' men continued to drive forward and forced a series of dangerous set-pieces which the Wednesday defence did well to repel.
Substitute Matthew Green headed a McNaughton cross just over the bar moments after coming on in the 81st minute, and Paul Parry also skewed a late effort high and wide of target.
Walton was issued his straight red card two minutes later for his awful challenge on Gilbert, which sent the Wednesday man cartwheeling dramatically through the air.
Then deep into injury time Cardiff were denied one final time when another firm Johnson header was headed off the line by the outstanding Steve Watson.
Teams:
Cardiff Forde, McNaughton, Purse, Johnson, Ledley,Whittingham (Thompson 75), McPhail, Walton, Parry,Feeney (Green 82), Chopra.
Subs Not Used: Alexander, Flood, Gunter.
Sent Off: Walton (90).
Booked: Purse.
Goals: Johnson 45.
Sheff Wed Turner, Bullen, Watson, Wood, Gilbert, Tudgay,Whelan, Lunt (Folly 84), Brunt, Clarke (Lekaj 90),Burton (MacLean 86).
Subs Not Used: Adamson, Spurr.
Booked: Whelan, Wood, Burton.
Goals: Clarke 39, Burton 67.
Att: 13,621
Ref: M Russell (Hertfordshire).