The two teams cancelled each other out, creating little danger in front of the goal for the first hour and spending most of their energy on trying to shut down the opposition.
Rubin midfielder Aleksandr Ryazantsev had the best chance to break the stalemate in the first half but his powerful header on the run was well saved by Panathinaikos keeper Alexandros Tzorvas five minutes before the break.
Ryazantsev also wasted a good opportunity midway through the second half when he could not control the ball after being sent clear on goal by Brazilian team-mate Carlos Eduardo.
Rubin coach Kurban Berdyev went for broke with time running out, introducing speedy Turkish striker Gokdeniz Karadeniz and creative Nigerian forward Obafemi Martins, but the visitors withstood a furious late rally and twice cleared the ball off the line.
At the other end, Panathinaikos substitute Lazaros Christodoupoulos could have snatched the points for the Greek champions against the run of play but twice missed the target in the last 10 minutes.
Berdyev was left to rue missed chances.
"We created enough chances to win but unfortunately could not put away any of them," he told reporters.
"Martins and Karadeniz boosted our game significantly after coming on but still could not score."
The draw left both teams with only a slim chance of reaching the knockout round. Third-placed Rubin trail FC Copenhagen by four points after the Danish champions held group leaders Barcelona to a 1-1 draw in the other Group D match.
Panathinaikos remain bottom of the group with two points.
"The draw was a fair result tonight, just like it was in Athens," said Panathinaikos coach Nikos Nioplias.
"We still have a small chance of making the playoffs and we will fight for it to the very end."
