That became clear after Saturday's 3-1 loss to Kristianstad in the final group-stage match.
Malmö also lost the opening group match to Piteå, 3-2. The Skåne side won the second match against Umeå 4-1, but finished third in the group with three points.
Kristianstad won the group with seven points from two wins and a draw, and advances to the cup playoffs.
Last season, Malmö came third in the women's Swedish championship as a newcomer; Kristianstad finished sixth.
