Traianos Dellas' side, who have appealed a three-point deduction for crowd violence, went into the final match hoping to get a win to at least give themselves a chance of survival ahead of next week's appeal hearing.
But after wasting several good chances to score and pushing forward in the closing stages, Atromitos caught AEK on the break.
Kostas Giannoulis' raced clear and finished clinically in the third minute of added time.
The goal ended any hopes that AEK had of remaining in the top flight, with several players breaking down in tears at the final whistle. Even if hey win their appeal, they are two points short of safety.
AEK - who have had financial problems and saw key player Giorgos Katidis banned for making a Nazi-style salute during a league match - join bottom club Kerkyra in next season's Football League, Greece's second tier.
"There are no words to describe my feelings," a dejected AEK coach Dellas told reporters.
"The guys really gave it a go, and much like AEK, they do not deserve a fate like this. I'm so sorry as well, I tried my best to raise morale but I didn't manage to succeed. I feel deep sorrow for what has happened, but we have to try to think about the next day and the future of the club."
Dellas, a former player with AEK and Euro 2004 winner with Greece, was only brought in 11 days ago for the final two matches, his appointment representing a last throw of the dice for a club desperate to avoid the drop.
The defeat left them two points adrift of safety, or five if the three-point penalty is upheld, ending any hopes they had of remaining in the top flight.
The Super League's disciplinary committee dished out the punishment last Friday after AEK's match against Panthrakikos at the Olympic Stadium was abandoned due to a pitch invasion by home fans.
The league said the match would be recorded as a 3-0 loss for AEK, applied a three-point deduction from this season's tally and two from the next campaign, and slapped the club with fines totaling 4,000 euros.
The club submitted an appeal against the decision, which it called a "pre-meditated crime by a corrupt system" in a strongly worded statement, which is set to be heard next week.
At the other end of the table, Panathinaikos failed to finish in the Champions League playoff places despite running out 3-2 winners at the Olympic Stadium against Veria thanks to two goals from Spanish midfielder Victor Vitolo and a Habib Sow effort.
Champions Olympiakos Piraeus also tasted victory in their final match, seeing off Panionios 2-1.
Kostas Mitroglou put them ahead after 12 minutes, but the visitors responded strongly and equalised eight minutes later through Andreas Samaris.
The hosts' quality showed in the second half, however, and Greece defender Avraam Papadopoulos headed home what proved to be the winner in the 72nd minute to ensure the Reds ended the season on 77 points from 30 matches.
The end-of-season playoffs, which determine Greece's second Champions League spot and Europa League representatives, will be contested between PAOK Salonica, Asteras Tripolis, Atromitos and PAS Yiannina.
PAOK ended their regular campaign with a deserved 2-0 home win over Yiannina thanks to second-half goals from Giorgos Georgiadis and Kostas Katsouranis to finish as runners-up in the table.