The Yellows failed to impress against a largely defensive PAOK side in the first half but the second 45 was a different story.
Good work by Nacho Skoko set up Gustavo Manduca for the only goal of the game in the 48th minute of the game.
AEK had a couple of chances to finish the visitors off but squandered them, ensuring that their fans endured another nervous night until the final whistle.
The win moves Dusan Bajevic's men into fifth place on 18 points, while PAOK stay 21 points in third place.
Ergotelis came away with all three points from Iraklis's Kaftantzogleio Stadium thanks to two second-half goals.
Dimitris Orfanos got the first on the 50-minute mark and, as Iraklis went in search of an equalizer, Mario Budimir double the lead on 84 minutes.
The result leaves Iraklis hovering just two points above the relegation zone while Ergotelis are sitting comfortably in sixth on 17 points.
In Saturday's other game Asteras Tripolis and Xanthi fought out a 0-0 draw in the Peloponnese.
The Greens had to wait more than hour before Levadiakos's resistance was finally worn down. Defender Loukas Vintra rose to head a 67th minute corner against the legs of Levadiakos goalkeeper Nikos Karakostas and then watched as the ball trickled into the net. It was scrappy but PAO coach Henk ten Cate was not complaining.
He would have been ecstatic about the second goal, which secured all three points but also showed that the Greens can play some neat football.
French striker Djibril Cisse scored it in the 81st minute when he latched onto a sublime through ball from Gilberto Silva and stroked the ball past Karakostas.
The win means that Panathinaikos have 28 points after 10 games while Olympiakos are in second on 26.
Olympiakos were held to a 1-1 draw by Iraklis on Saturday thanks to an injury-time goal from teenager Apostolos Vellios.
The champions, missing several players through injury, took the lead in the 40th minute thanks to a powerful shot by Enzo Maresca from the edge of the area.
Then, much to the anger of the home fans, a Costas Mitroglou goal ruled out although replays showed no offense was committed. Dudu also hit the bar late on.
Olympiakos were made to pay when Vellios connected with a Dennis Epstein cross and saw the ball bounce into the ground and over the arms of Antonis Nikopolidis. It was the least Iraklis deserved after a late surge in the game, indicating that the return of Savvas Kofidis on their bench is already having the desired effect.
The game ended with Olympiakos players and officials surrounding the referee to complain about his decision to disallow Mitroglou's goal.
PAOK went clear in third place with a 2-1 win away to basement boys Panthrakikos. The Thessaloniki team's goals came from Vierinha and Pablo Garcia. Bedi Buval replied for the hosts who remain bottom of the league with just one point.
PAOK are on 18 points after 10 games, three ahead of local rivals Aris who were held to a 0-0 home draw by Kavala on Saturday despite the visitors having three players sent off in the second half.
Aris had more than 20 attempts at goal and hit the post and the bar during the game but were unable to break down the resistance of Kavala, this season's surprise package.
The new Aris manager Hector Raul Cuper watched the game from the stands and will have been impressed by his side's build-up play but knows that he needs to improve his players' finishing.
On Sunday, Daniel Cesarec scored a hat-trick as Asteras Tripolis beat PAS Yiannina 3-0. Cesarec is the Super League's top scorer with 10 goals.
Bosko Balaban did his best to keep up with the Croation by scoring two for Panionios as they won 2-1 at Xanthi.
Atromitos and Ergotelis drew 0-0 in Athens, leading to the home fans barracking their own players, coach and officials.
AEK take on Larissa on Monday afternoon.
P W D L F A Pts
1 Panathinaikos 10 9 1 0 20 5 28
2 Olympiakos 10 8 2 0 17 4 26
3 PAOK 10 5 3 2 12 6 18
4 Kavala 10 4 3 3 11 8 15
5 Aris Salonika 10 3 6 1 10 8 15
6 Ergotelis 10 3 5 2 15 12 14
7 Asteras Tripolis 10 4 2 4 13 13 14
8 Panionios 10 4 2 4 12 11 14
9 AEK 9 3 3 3 10 10 12
10 Iraklis 10 3 2 5 8 11 11
11 Larissa 9 2 4 3 10 13 10
12 PAS Yiannina 10 2 4 4 8 13 10
13 Xanthi 10 3 1 6 6 10 10
14 Atromitos 10 2 3 5 9 10 9
15 Levadiakos 10 2 2 6 6 17 8
16 Panthrakikos 10 0 1 9 6 22 1
Cisse double sends PAO top
Greens join Olympiakos in first place
Greek Cup 2009-2010
Third and Fourth Round results and fixtures
More Super League clubs drop out
Larissa, Panthrakikos and Ergotelis lost
Olympiakos beat Ergotelis at the death
Dudu scores winner five minutes from full time
Olympiakos beat Asteras to go top
Reds take over top spot, Panathinaikos play on Sunday
Cisse double makes it six for PAO
Olympiakos two points behind but AEK beaten by Xanthi
PAO beat AEK to stay clear at top
Perfect start for Greens, as Olympiakos win as well
Katsouranis makes it four in a row for PAO
Panathinaikos stay on top of the table with their fourth successive win
PAO clear at top, Reds suffering
Greens beat Panthrakikos, Olympiakos held by Kavala
Fan incident mars Iraklis vs Aris corker
Thessaloniki derby ends all square after Campora double strike
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