Johnson faced strong competition from Peter Taylor, who guided Hull City to the top last night with a 1-0 win over Swansea. Taylor's troops also beat Southend, Rochdale and Kidderminster and drew at Doncaster and Leyton Orient in September.
Swansea's Brian Flynn was not in the running for the award for a second consecutive month after losing twice and drawing once.
Meanwhile, Peter Taylor is currently joint-7th best in the country in the TISSOT Manager Performance League (click here to view in full).
Elsewhere, Nigel Worthington (Norwich), Phil Parkinson (Colchester) and Martin Allen (Barnet) picked up the manager of the month awards for their respective divisions.