Hen Ezra and Hanan Maman put Hapoel 2-0 ahead before half-time and Maor Melikson added a third just after the break before Rauno Alliku scored a late consolation for the Estonians in the Turner Stadium on Tuesday night.
Hapoel manager Barak Bakhar said: "We made it look easy against the Estonians but it will be a very different story against Zagreb.
“We will have to raise our game and we saw what Croatian football is all about during the World Cup. We will prepare ourselves tactically and come ready."
Hapoel will play in Zagreb next Tuesday, with the return in Beer Sheva the following week.
