J fixture against a side reeling from the sacking of their captain Kostas Katsouranis after Michael Dawson's first half header.
But their Greek hosts battled back to scrape an unlikely draw after the break courtesy of Spanish striker Toche.
With Lazio beating Slovenian outfit Maribor 1-0, missing a penalty in the process, Spurs slipped to third place behind their Serie A rivals who had Ederson to thank for their win.
Elsewhere Lyon prevailed in a seven-goal thriller in Israel against Hapoel Kiryat Shmona, Gueida Fofana bagging the injury time winner to earn the former multiple French champions a breathless 4-3 win.
Last season's beaten finalists Athletic Bilbao fell 3-1 at Sparta Prague, while there was joy for two Bundesliga sides - with Bayer Laverkusen and Hanover prevailing against Rosenborg and Levante respectively.
At Panathinaikos, France's number one keeper Hugo Lloris made only his second start for Spurs in place of the rested Brad Friedel.
Lloris was one of three changes from the side that toppled United, with Dawson coming in at defence for William Gallas and made captain for the night. In midfield Tom Huddlestone replaced Sandro, who dropped to the bench.
After enjoying the bulk of possession early on Tottenham took a 35th-minute lead when Dawson headed in Huddlestone's curling free kick at the near post.
As half-time beckoned Lloris was fortunate to get away with dropping an attempted catch from a ball coming in from the right, the £8 million (9.9 million euros) signing from Lyon last month hastily making amends for his error.
After the restart Jermain Defoe had a chance to seal the game but his shot from the edge of the box went over the bar. Panathinaikos were let off the hook again after the hour when Defoe's deflected 20 yard shot narrowly went wide.
On 76 minutes the Greeks stole an equaliser, against the run of play, when Toche ran onto a great through ball from Giourkas Seitaridis to round two defenders and shoot past Lloris into the far corner.
That set up a nervy final quarter of an hour for the Premier League highflyers, who held on for a point, although three were in the offing.
Inter Milan, who face AC Milan in the San Siro derby this weekend, maintained control of Group H with a 3-1 win in Azerbaijan against Neftchi, the goals all coming in the first half from Brazilian Philippe Coutinho, Joel Obi and Marko Livaja.
Former Inter and Barcelona star Samuel Eto'o inspired big-spending Russian outfit Anzhi Makhachkala to a 2-0 win over Swiss outfit Young Boys, the Cameroon striker converting a 62nd minute penalty and doubling up on the whistle.
That pushed Anzhi up to the top of Group A but Liverpool can regain the summit with victory over Udinese at Anfield later.
Also in action later were reigning champions Atletico Madrid, up against Czech side Viktoria Pizen, while Marseille hosted Limassol of Cyprus and another French club, Bordeaux, faced Newcastle.