Juan Ramon Rocha's cash-strapped team, who must defeat Spurs at White Hart Line on Thursday to progress to the knockout stage, had Antonis Petropoulos to thank for the victory.
The 26-year-old, nicknamed 'Petrogoal' by the Panathinaikos fans, opened the scoring with a low drilled shot in the 24th minute and Loukas Vintra added a second with a long-range free kick.
Panionios pulled a goal back 12 minutes from time through Markos Dounis but Panathinaikos held firm to claim only their fifth win of the season from 13 matches and climb to sixth place, 16 points adrift of champions and arch-rivals Olympiakos.
"We wanted the three points badly because we have fallen behind in the standings and we had a very good performance today, although perhaps our minds were already on the Tottenham game," Petropoulos told reporters.
"We will give everything to beat Tottenham and get the qualification. It's a given that they are difficult opponents and will have home advantage, but Panathinaikos always likes to chase these kinds of games and if have a good day then I hope we can get the result we need and qualify."
Olympiakos warmed up for their final Champions League group fixture with Arsenal by opening up a 10-point lead ahead of PAOK Salonika following a 2-1 home win over Platanias on Saturday.
With one eye on Tuesday's match with the Gunners, who need victory and for Schalke to slip up against Montpellier to claim top spot in Group B, Leonardo Jardim's came away with three points after taking a 2-0 lead inside 20 minutes thanks to Djamel Abdoun's penalty and a Vassilis Torosidis strike.
Shikoze Udoji pulled a goal back with a superb strike from distance shortly before halftime and although the visitors had chances to level matters, the champions held on to record their seventh successive home win of the season.
AEK Athens host PAS Giannina on Monday hoping to turn around a woeful start to the season and move off the bottom of the table.
- Sports & Recreation
- Juan Ramon Rocha
- Antonis Petropoulos