The win at the Olympic Stadium in Athens proved to be controversial as the visitors felt they had a perfectly good equaliser ruled out.
Sotiris Ninis gave Jesualdo Ferreira's men the lead in the 20th minute when he was left umarked in the box to volley in a cross. It was the highlight of a bright performance from the winger.
It was a shame there was nobody there to witness it as the game was being played behind closed doors.
Djibril Cisse had a goal correctly ruled out for offside early in the second half but the game's most controversial moment came in the 68th minute when Michel appeared to have equalized with a free header but the referee blew for a foul off the ball, much to the anger of Aris.
The three points were not secure for Panathinaikos until injury time, when Alexis Tzorvas produced a fine save to deny Javito. Reports on Saturday indicated that the Spanish forward will be on his way to Olympiakos at the end of the season.
The win means that Panathinaikos have 37 points from 17 games, with Olympiakos on 39 and due to play Kerkyra on Sunday.
Aris are sixth on 23 points.
They were overtaken by Kavala, who beat struggling Larissa 1-0 at home. Serge Die scored the only goal of the game with a typically stunning finish in what proved to be a niggly game that led to the referee showing nine yellow cards.
Larissa's prospects of staying up are looking increasingly bleak as they remain on 11 points, five adrift of the others.
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