Diego Simeone's men progressed to the next round with a narrow win over the already eliminated Israeli side at Vicente Calderon
Raul Garcia's well-taken goal, after just seven minutes would prove to be difference between the two sides, in a largely defensive and turgid encounter.
Diego Simeone made eight changes from the game against Granada at the weekend, as he celebrated his 50th official game in charge of the holders. A typically weakened side, with the likes of Jorge Pulido, Domingo Cisma and Silvio handed starts.
After a controlled start, it took just seven minutes for the hosts to break the deadlock. Adrian Lopez's measured cross was poorly judged by goalkeeper Apoula Edel, as Emre took control to tee up Raul Garcia, who fired into the net.
Hapoel took a while to adjust themselves, but spurned a great chance soon after going behind. Roei Gordana's fine delivery from a corner saw Hanan Maman rise highest to power a header towards goal, but somewhat cruelly, it had flashed the wrong side of the post.
Atletico looked noticeably lethargic and disjointed as they suffered a shock 2-0 reverse at Academica two weeks ago, but there would be no such problems against the already-eliminated Israeli side. Adrian should've doubled his side's lead after a defensive mistake, but saw his tame effort blocked by Apoula.
Hapoel improved as the first-half progressed, and were unlucky not to be level as Tal Ben-Haim latched onto a fine pass from midfield, but against an acute angle, saw his shot evade Sergio Asenjo and into the side-netting.
Los Colchoneros could not exactly penetrate a solid back four, as Adrian struggled to test the opposition goalkeeper, with the attacking tempo soon significantly dropping.
Josef Abuksis' men were nevertheless, still in the game with a one-goal deficit, and were once more denied. Ben-Haim stumbled after controlling the ball past a static defence, but Asenjo's fine block at the feet of the striker would ensure his clean sheet would remain intact.
Simeone's charges were largely restricted for long periods of the second half, as neither side could fashion real goalscoring changes. A measured pass from midfield carved out an opening for Adrian, but the striker could once more not divert the ball past an on-rushing Apoula.
Despite the performance, the result was enough to qualify from Group B alongside Viktoria Plzen, as the holders now turn their attention to La Liga and an encounter with Sevilla on Sunday.