In 1959, the VFL competition consisted of twelve teams of 18 on-the-field players each, plus two substitute players, known as the 19th man and the 20th man. A player could be substituted for any reason; however, once substituted, a player could not return to the field of play under any circumstances. Teams played each other in a home-and-away season of 18 rounds; matches 12 to 18 were the "home-and-way reverse" of matches 1 to 7. Once the 18 round home-and-away season had finished, the 1959 VFL Premiers were determined by the specific format and conventions of the Page–McIntyre system.
*As a consequence of its 1981 decision to change its rules relating to tied Brownlow Medal contests, the AFL awarded a retrospective medal to Verdun Howell in 1989.
The VFL threatened to move matches away from Windy Hill and the St Kilda Cricket Ground at the start of the season owing to a dispute with the Essendon and St Kilda Cricket Clubs. Cricket club members were entitled to purchase football club season tickets for one third of face value, but 1957/58 cricket club members had paid for their 1958 football tickets at 1957 prices instead of 1958 prices. Following a ruling by the state Minister for Lands, the cricket clubs paid the balance in mid-April, and no matches were moved.
The committee of the Essendon, fifth on the ladder at the end of 1958, took the innovative step of employing Bert Willee, the chief lecturer in physical education at the University of Melbourne, to design and supervise the delivery of a carefully planned programme of physical training for each player, taking into account the special requirements of each playing position, as well as concentrating on the special needs of each individual player. Essendon played in the 1959 Grand Final, having finished the season in fourth place.
From 1959, VFL Second Eighteens' matches and were played as curtain-raisers to seniors matches, having previously been played at the same time as the seniors at a different venue. The Third Eighteens' matches were now played at a different venue to the seniors, having been played as the main curtain-raiser until 1958.
The VFL introduced the premiership cup, to be awarded to the Premiership team immediately after the Grand Final Match.
As Carlton team was running down the players race at the Brunswick Street Oval before the start of its round 10 match against Fitzroy, Carlton centre half-backBob Crowe stumbled and fell, badly injuring his knee. A short time after the match began, it was obvious that Crowe was in great pain and was totally unable to keep up with the play. Carlton appealed to the field umpire, and they were allowed to substitute one of their reserves for Crowe, even though he had taken the field.
The Collingwood Secretary, Gordon Carlyon and four Collingwood footballers received death threats before the Round 14 match against Carlton that are thought to have been connected with a potential betting plunge.
Despite losing its first five matches, the 1958 premiers Collingwood reached the final four.