Raul Garcia's fifth goal of the season after just seven minutes was enough to take all three points as the Spanish side were not punished for their profligacy in front of goal by a struggling Hapoel side who have taken just one point from their five group matches.
Atleti however are not yet guaranteed top spot in Group B which would ensure they are seeded in the next round as they still need a draw from their final game away to Viktoria Plzen to finish ahead of the Czechs.
As is customary in the Europa League, Diego Simeone made eight changes from the side that won 1-0 at Granada at the weekend but it was two of those who retained their place that combined for the opening goal as Adrian burst down the right and after Apoula Edel had parried his cross, Emre turned the ball back for Garcia to sidefoot in off the underside of the bar.
However, despite a rough start the Israelis should have been level within six minutes as Roei Gordana rose highest to meet Gil Vermouth's corner but just headed the wrong side of the post.
Adrian should then have given Atleti some breathing space as he broke clear on Apoula on 18 minutes but placed his shot far too close to the keeper.
Apoula was tested again just before half-time by a shot from range by Emre but again the keeper palmed the ball away and Diego Costa's follow-up effort was blocked.
Atleti though were struggling to put Hapoel away and the visitors could easily have equalised with the first major opening of the second-half as Tal Ben Haim wriggled clear of a couple of Atleti challenges on the edge of the box but just overran the ball slightly allowing Sergio Asenjo to come off his line and block the ball away to safety.
Garcia immediately had a decent chance to double his tally at the other end but headed straight at Apoula, whilst Adrian also had another two decent opportunities to seal the three points but after heading over from close range, he too was denied by a brave stop from Apoula.
The hosts were frustrated by the visiting keeper once more four minutes from time as he reacted brilliantly to turn Garcia's well-executed volley over but his heroics did not count for anything as Atleti held on without any further scares.