Khalatbari struck just before the hour mark as Zobahan won their fourth game in the group stage and set-up an all Iran clash with Mes Kerman in the knockout stage of the tournament.
The defeat for Al Ittihad, meanwhile, means the two-time ACL champions from Saudi Arabia miss out on a place in the next round as they finish third with Bunyodkor’s 4-1 over Al Wahda cementing second place for the Uzbeks.
Following Bunyodkor’s victory, Al Ittihad needed to win to avoid elimination but lacked urgency in the opening exchanges with chances at either end at a premium for much of the first half.
Hasan Ashjari launched a speculative effort from distance that sailed over the bar to highlight a relatively quiet opening 15 minutes and it took a further 11 minutes before there was another chance of note, although Mohammed Noor was unable to get any direction on a header for Al Ittihad before Sultan Alnumare volleyed wide.
Saud Khariri sent a free-kick over the bar in the 35th minute while Alnumare dragged a shot wide soon after for the visitors while Khalatbari should have done better for Zobahan when he headed wide with the keeper stranded just before half time.
Al Ittihad had the post to thank six minutes into the second half for keeping them level when Mohsen Mosalam’s low shot from outside the box struck the bottom of the left upright before the Iran international directed his shot from the rebound wide of the goal.
But the hosts took the lead after 58 minutes when Khalatbari pounced on a terrible back-pass before rifling an unstoppable drive into the back of the net.
Zobahan almost had a second minutes later when Sina Ashoori's long-range drive had goalkeeper Mabrouk Zaid at full stretch to push the ball away for a corner.
That chance seemed to rattle Al Ittihad into action and Hamad Al Montashari saw his bullet header parried away by Gordan Shahabaldin for a corner after 68 minutes.
Al Ittihad came even closer soon after when Al Montashari’s curling shot was palmed back into the dangerzone by Shahabaldin where Talal Al Meshal knocked it back goalwards only for Farshid Talebi to hook the ball off the line.
Noor’s free-kick was deflected wide in what was ultimately Al Ittihad’s last chance of the game as last year’s AFC Champions League finalist’s campaign came to an early end.