The win sees Hapoel draw level on points with Southampton who were beaten by in Group K.
Hapoel travel to St. Mary's to take on Southampton on December 8 in a match that will decide second place in the group.
Goals from Aleksandr Kokorin and Aleksandr Kerzhakov condemned Maccabi Tel Aviv to a 2-0 defeat against Group D winners Zenit in St. Petersberg.
GROUP K STANDINGS
1. Sparta Prague Pl. 5, W. 4, Pts. 12
2. Southampton Pl. 5, W. 2, Pts. 7
3. Hapoel Beer Sheva Pl. 5, W. 2, Pts. 7
4. InterPl. 5, W. 1, Pts. 3