Jones beat off competition from Bristol City's Gary Johnson, Owen Coyle of Burnley and Glen Roeder of Norwich to take the trophy.
"Football management is a precarious job and this award shows how things can change very quickly," said Jones.
"We are in a business that is emotionally run and sometimes people's emotions run higher than they should.
"Thankfully we've turned it around and everyone loves us again but it has been a team effort, the camaraderie here is great.
"Awards are always satisfying and it is something to show the boys for all of their hard work.
"The award is a big pat on the back for the team but it is early days, we want to win trophies at the end of the season."