Both sides threatened from set-pieces in the first period and that continued after the break with Richard Naylor and Sam Sodje both going close with headed chances for the visitors.
Naylor saw his effort well blocked by Stockdale and Sodje sent an effort inches wide.
But Nigel Pearson's side created the better opportunities and keeper Casper Ankergren twice made fines saves from Andy King, the second after a fine lay-off from Howard.
The excellent Lloyd Dyer also teed up Matt Fryatt and Howard also had two good headed chances from corners before his dramatic late winner.
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