Having beaten Scotland 2-1 in Haifa earlier in the week, Israel moved three points clear after a polished performance.
Goals from Brighton striker Tomer Hemed, who is currently on loan at QPR, and Dia Seba earned Israel victory.
Hemed opened the scoring after eight minutes with a route one goal, after a big clearance from the goalkeeper sent him clear, and he rolled the ball through the legs of the Albanian No. 1.
Seba secured the win with a deflected effort seven minutes from time, much to the delight of the home fans in Beer Sheva.
NATIONS LEAGUE GROUP C1 STANDINGS
1. Israel Pl. 3, Pts. 6
2. Scotland Pl. 2, Pts. 3
3. Albania Pl. 3, Pts. 3