AEK's Cameroon striker Steve Leo Beleck continued his rich vein of scoring form by grabbing the only goal of the game in the 76th minute at the Olympic Stadium, volleying home from inside the box following a clever lobbed assist by Jose Carlos.
It was the 18-year-old striker's fifth goal in 11 league outings to date, with the win moving AEK to 25 points from 12 matches.
Panathinaikos had been expected to re-claim top spot but instead slumped to a 3-1 reverse at Aris.
Jesualdo Ferreira's team went behind to Daniel Cesarec's 12th-minute strike from close range but drew level before half-time via Jean-Alain Boumsong's bullet header from Sebastian Leto's free-kick.
However, second half strikes from Francis Dickoh and Neto, who curled in a spectacular free-kick, stunned the Greens who lie third with 23 points from 10 matches.
Olympiakos Pireaus are second just one point adrift with a game in hand after Ernesto Valverde's team bounced back from last weekend's 2-0 loss at Asteras Tripolis by seeing off 10-man Panetolikos 2-0 at home on Saturday to move to 24 points from 11 matches
It took a mediocre Olympiakos, who host Arsenal on Tuesday in their crucial final Champions League Group F match, just over an hour to break the deadlock at the Georgios Karaiskakis Stadium.
Stubborn Panetolikos held on until Andre Rocha upended Djamel Abdoun in the box, which led to a penalty and a red card for the offender.
Marko Pantelic duly converted the spot-kick, while the Reds' striker Rafik Djebbour made it 2-0 in the 74th minute, although television replays showed the Algeria forward had started from an offside position.
