After the dissolution of the NSL, South Melbourne and the Melbourne Knights were initially left without a league to play in.

In 2004, South faced potential liquidation, partly after being left with no league to play in, and no revenue. However, in 2005 the club was accepted into the Victorian Premier League and began a new era in the shadow of the A-League.
South’s first game in the competition was a 0-0 draw against Heidelberg in front of over 11,000 people at Bob Jane Stadium. John Anastasiadis was coach of the team, and Vaughan Coveny was the captain.
South managed to nab their first win in the competition in round 2, with a 1-0 win against St Albans. The form would continue with 5 wins in the next 6 games.
South’s largest win of the season was a 4-0 drubbing of Fawkner-Whittlesea in round 12, and it didn’t lose any of its matches by more than a goal during the season.
South romped past Altona in the elimination final with a 3-0 win, lost to Green Gully in the semi-final, and was eventually eliminated by Heidelberg in the preliminary final.
It may not have ended in silverware but the 2005 season was a celebration of the club’s survival.
| Team | Pts |
| Green Gully | 49 |
| Heidelberg United | 47 |
| South Melbourne | 46 |
| Fawkner-Whittlesea | 43 |
| Oakleigh Cannons | 40 |
| Altona Magic | 40 |
| Preston Lions | 39 |
| Essendon Royals | 37 |
| Melbourne Knights | 33 |
| Bulleen Zebras | 28 |
| Frankston Pines | 28 |
| Sunshine George Cross | 24 |
| St Albans Saints | 23 |
| Bentleigh Greens | 16 |

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