Jesualdo Ferreira's team gained revenge for their Greek Cup loss to AEK by defeating their rivals at the Olympic Stadium to stay within seven points of Olympiakos, whose 2-1 win at Aris Salonika on Saturday moved them on to 57 points from 22 games.
Goals from Greece international Kostas Katsouranis and Loukas Vyntra gave the Greens a two-goal lead before AEK's Nacho Scocco pulled one back.
French striker Djibril Cisse sealed the points for the champions with his 18th goal of the season 15 minutes from time.
"We have to win at the Karaiskaki to close the gap on Olympiakos and keep our title hopes alive," Cisse told reporters. "I want to score on Saturday because it will be a special match."
Ferreira has kept the champions in contention after taking over from Nikos Nioplias in November.
"For us the only option is victory (against Olympiakos). "I'm sure the Olympiakos players know that Panathinaikos can win this race and I hope there will be a referee who will stand up to the challenge," he said.
Ernesto Valverde's Olympiakos recorded their 11th win in succession at Aris, Spanish midfielder David Fuster scoring the winner with an overhead kick in the 75th minute for his eighth goal of the season.
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