Kevin Blackwell's side had been trailing to a 17th-minute goal from Robbie Savage as Nigel Clough's Derby side dominated the game.
United, without key defenders Chris Morgan and Andy Taylor, mounted a last-ditch challenge as Williamson pounced to leave the Sheffield side in seventh place, pushed out of the top six on goal difference.
Derby, with four wins from their last five games, started in confident fashion, Kris Commons cutting in from the right flank before pumping over a low cross. Former United striker Rob Hulse slid in to connect but dragged the ball wide of the target.
New boy Mark Yeates almost crowned his home debut with a goal for the Sheffield side minutes later, surging into the area only to see his fierce strike blocked by Stephen Bywater. Lee Williamson lashed in the rebound but it was blocked by Shaun Barker.
Derby snatched the lead with a stunning goal on 17 minutes. A poor clearance fell to veteran midfielder Savage who hammered the ball past a stunned Mark Bunn from 30 yards.
The Pride Park side almost grabbed a second with United in disarray, Commons outpacing Jordan Stewart as he fired in a low drive from a tight angle, the ball being beaten away at the near post by Bunn.
United crumbled again. Ex-United midfielder Michael Tonge steamed in from the right but his shot from eight yards was blocked by Bunn.
Tonge, on loan from Stoke City, carved out another opportunity, his looping cross finding Paul Green. The midfielder's volley beat Bunn but dipped the wrong side of the bar.
Former Wigan striker Henri Camara came on for the ineffective Darius Henderson and the move almost produced an immediate result.
Stewart fired in a long-range strike that was pushed away by the diving Bywater. Camara pounced only to see the Derby keeper fling out a hand to deflect the ball around the post.
With seconds to go, Yeates cut inside from the right and squared the ball to Williamson who drilled a low shot into the bottom right-hand corner.