The former Brazil international slotted home in the 75th minute at the Olympic stadium to clinch three points for the Greens, who are now in the driving seat heading into the final round of matches on Wednesday.
Although Panathinaikos now lead the table with 10 points with just one game to play, the race to secure Greece's second Champions League spot remains wide open as PAOK are second on nine points, while AEK Athens are a further point adrift in third.
Gilberto, who joined Panathinaikos from Arsenal in 2008, is set to play his last game for the Greens against AEK in their final play-off fixture.
The 34-year-old midfielder is out of contract after the conclusion of this season and is expected to return to his native Brazil, although he hinted that he could stay on in Greece.
"All that remains now is for us to secure the Champions League place," Silva told reporters.
"From the first day that I came here I have felt at home and I will tell my children one day that Greece was very good to me, whether I leave or stay another season."
AEK suffered a surprise 1-0 defeat at Olympiakos Volos, Slovakian defender Peter Dolezaj on target six minutes from full time. Olympiakos Pireaus won the Greek title in March.
