The 1958–59 Liga Alef season saw Bnei Yehuda win the title and promotion to Liga Leumit.
A promotion-relegation play-off between the 11th and 12th placed clubs in Liga Alef, Maccabi Sha'arayim and Hapoel Afula, and the second placed clubs of the regional divisions of Liga Bet, Hapoel Netanya and Hapoel Be'er Sheva. Each club played the other three once.
Shortly after the Relegation play-offs, Hapoel Afula was disqualified for fielding Zvi Singel, who was also listed at the Israeli football association as a player of lower division club, Hapoel Beit HaShita. as a result, Afula lost their Liga Alef status, and Hapoel Netanya took their place in Liga Alef.