Bednar struck in the third minute of stoppage time when he headed home a right-wing cross from Gianni Zuiverloon to earn Albion their first win in 11 games after a dismal run of just two points from a possible 30.
Albion had looked to be on course for a priceless victory when £3.5million striker Luke Moore gave them a 69th-minute lead with his first goal in 23 appearances since his arrival from Aston Villa, initially on loan, in February.
All that hard work then appeared to have been wasted when substitute Felipe Caicedo equalised for City four minutes from time.
But Albion were not to be denied and Bednar popped up with his fifth goal of the season to move them to within four points of safety.
While Bednar's strike couldn't have been better timed for Albion, it has turned up the heat on Hughes who faced taunts about his future from both the City and Albion fans.
City remain rooted in the relegation zone and have now won just one of their last nine league games, casting a major cloud over the position of Hughes.
They were dominant enough at times to have beaten Albion but their lack of a cutting edge, in the absence of the injured Robinho, proved to be their undoing.
City made a flying start thanks largely to Shaun Wright-Phillips, but they were unable to turn that early dominance into a breakthrough.
England winger Wright-Phillips was a real handful for Albion left-back Paul Robinson and had a fifth-minute shot blocked.
Vincent Kompany then tested Scott Carson from long range before Albion's defence was cut open by a swift three-man break.
Benjani and Darius Vassell combined in the 21st minute to set up Wright-Phillips, but his shot from the edge of the area flashed just wide.
Having overcome that early City storm, Albion gradually worked their way into the game and were inches away from breaking the deadlock on the half-hour through Bednar.
Jonathan Greening won the ball in midfield and Bednar exchanged passes with Robinson before surging into the area.
Bednar beat Joe Hart with a low drive but the ball cannoned off the foot of the post before luckily bouncing to safety off the back of the England goalkeeper's head.
City should have taken the lead in the 53rd minute only for Wright-Phillips to waste a golden chance when he drove the ball straight at Carson.
Albion took full advantage of the let-off when James Morrison split the City defence and Moore strode forward to roll the ball under Hart to score his first goal since his strike for Villa at Bolton in October 2007.
It looked a goal good enough to end Albion's winless run but their defence went to sleep in the 86th minute when a long throw from Richard Dunne caused chaos and Caicedo back-heeled the ball home at the far post.
Albion could easily have wilted, but came surging back and were rewarded by Bednar's late strike.