Albion fans chanted ``You're getting sacked in the morning'' in the direction of Hughes, whose side remain in the relegation zone.
Luke Moore's first goal for the Baggies had given them the lead before City levelled six minutes from time, Scott Carson credited with an own goal after substitute Felipe Caicedo's backheel had struck a defender, the post and the goalkeeper before crossing the line.
But Bednar had the final say by heading home a right-wing centre from Gianni Zuiverloon to cause wild scenes of celebration.
The Albion fans continued to show their support for manager Tony Mowbray and after 68 minutes their faith was rewarded when Moore scored the opener.
James Morrison threaded a pass through to the former England Under-21 player who kept his cool before sliding the ball past Joe Hart.
It was his 23rd appearance since moving from Aston Villa in January, initially on loan before completing a £3.5million switch in the summer.
Moore was taken off after 73 minutes and replaced by Craig Beattie, but with six minutes left Caicedo levelled matters with an audacious backheel which took a deflection and struck the post and Carson before crossing the line.
But in injury-time Bednar headed the winner from a Zuiverloon right-wing cross.