Herea headed home 10 minutes into the second half and, though the hosts had chances to equalise, Rapid held on for three Group C points.
Rapid made much of the early running, with Cassio first to try his luck although it provided catching practice for Hapoel keeper Edel Apoula.
Hapoel's Maaran Lala could not direct Omri Kende's cross goalwards after 15 minutes, but much of the action was at the other end.
Ciprian Deac fired wide from 12 yards, then took a corner which found Marcos Antonio but the Rapid captain headed wide.
Rapid keeper Danut Coman was given a comfortable save when Omri Kende volleyed goalwards from 20 yards, while Cassio saw his close-range effort blocked by Walid Badir.
Hapoel came into the game more as the game passed the half-hour mark, as Lala could not find the target from Shay Abutbul's free-kick and Nosa Igiebor saw his shot blocked by Antonio.
Lala had another chance from Abutbul's cross but was again wayward and, as the hosts finished the half with a flourish they came close to scoring when an 18-yard hit from Toto Tamuz drew a fine save from Coman.
Mihai Roman shot wide two minutes after the restart while, at the other end, Melo Ezequias headed Abutbul's corner into the arms of Coman.
The goal came in the 55th minute when Herea found himself unmarked at the back post to head Rui Duarte's cross home.
If Apoula was helpless on that occasion he was anything but four minutes later as he produced a fine save to keep out Daniel Pancu left-foot strike from the edge of the box.
He denied Pancu again in more routine fashion after 72 minutes, before Avichai Yadin fired wide at the other end.
Hapoel had two great chances for an equaliser in the final 10 minutes.
First Salim Toama picked out Bevan Fransman with a free-kick, but his header was wayward.
Then, with three minutes to play, Coman denied Toama with a fine stop to keep out his 12-yard strike.