Atalanta were held by a last-gasp Apollon Limassol equaliser, so are just one point off qualifying for the Europa League Round of 32.
The result almost mathematically secured their place in the Round of 32, as Everton lost 3-0 to Olympique Lyonnais.
The Orobici are still unbeaten in the tournament. Papu Gomez was out of action and Andreas Cornelius not fully fit, while the hosts had Valentin Roberge suspended, plus Jander and Andrei Pitian injured.
Atalanta won 3-1 when these sides met in Bergamo a fortnight ago, the only defeat the Cypriots had suffered thus far.
Alex Da Silva drilled just wide, but Andrea Masiello should’ve done better when he flashed his finish across the face of goal from six yards.
Josip Ilicic failed to make the most of good work by Hans Hateboer to win back possession at the by-line, his finish deflected over the bar.
Alex again tested Etrit Berisha from distance, but Atalanta were gifted the opening goal when Alef jumped so clumsily that he accidentally fell on Ilicic and the referee gave a penalty, which the Slovenia international converted himself.
Apollon almost scored a bizarre own goal, as a clearance smashed Alef in the face to ricochet over the bar from six yards.
The Italians started the second half strong too, as Mattia Caldara knocked on a corner for Andrea Petagna’s header on to the inside of the far post.
Berisha tipped a strange Antonio Jakolis diving header over the bar, but Atalanta’s lead rarely looked in danger. In fact, Riccardo Orsolini’s effort on his European debut was palmed wide of the far post after a smart Petagna back-heel flick.
However, the Cypriots scored last-gasp equalisers against Lyon and Everton, so repeated the trick with almost the last kick of the game here. A long cross found Zelaya for a glancing header from six yards, but the point still sees Atalanta on the verge of qualification.
Apollon 1-1 Atalanta
Ilicic pen 35 (At), Zelaya 94 (Ap)
Apollon Limassol: Bruno Vale; Joao Pedro, Yuste, Alef, Vasiliou; Sachetti, Alex Da Silva (Maglica 76), Allan; Sardinero (Schembri 64), Zelaya, Papoulis (Jakolis 58)
Atalanta: Berisha; Masiello, Caldara, Palomino; Hateboer, Freuler, Cristante (De Roon 81), Spinazzola; Kurtic (Gosens 69); Ilicic (Orsolini 55), Petagna
Ref: Treimanis (LTV)