Lars-Christer Olsson has been chairman of Sef for nine years and has been criticized because, in connection with his resignation, he openly supported Sirius' chairman Ove Sjöblom as his successor.
The 32 clubs in the Allsvenskan and Superettan are the members of Sef and voted for their new chairman during Friday's annual meeting.
Two of them voted blank.
Of the rest, half voted for Andersson and half for Sjöblom.
As chairman of Sef, Jens T Andersson will also be elected to the Swedish Football Association's board.
Jens T Andersson is best known for having previously been CEO of AIK Football.