The 1949 VFL thirds season was the 4th season of the VFL thirds, the Australian rules football competition operating as the junior competition to the Victorian Football League (VFL).

Carlton won their second thirds premiership, defeating minor premiers Geelong by 11 points.

At the end of the previous season, North Essendon withdrew from the competition, and TAA − a side representing Trans Australia Airlines − took its place. However, the side was too heavily beaten and withdrew after round 4.^[1][2]

The demise of TAA meant most teams had an extra game counted in the standings. Hawthorn, Melbourne, North Melbourne and St Kilda − who all played and defeated TAA − remained at 16 games.^[3]