Chances were hard to come by at the OACA Spyros Louis stadium with the Russian outfit posing a greater attacking threat, striker Sergei Kornilenko going close on several occasions.
For Panathinaikos, Djibril Cissé was far too often isolated as the home side's lone striker in the absence of quality service from midfield.
The result leaves Panathinaikos with a difficult task to turn their campaign around as the Greens have collected just one point from three matches. Rubin remain third with two points from their opening three fixtures.
After suffering two successive defeats in their opening fixtures Panathinaikos, who went into the game shorn of the suspended Gilberto Silva and injury victims Sidney Govu, Sotiris Ninis and Sebastian Leto, started promisingly against their Russian opponents, controlling the early possession
But the Greens struggled to create chances and it was the hosts who threatened first in the 24th minute when Kornilenko headed Bebars Natcho's corner narrowly wide.
Rubin grew in confidence as the half wore on and the home side had Loukas Vyntra to thank after he blocked Kornilenko's shot on the line just before the half-hour.
Home keeper Alexandros Tzorvas then made a smart save from Alan Kasaev's strike from distance shortly afterwards.
Cissé missed an opportunity to open the scoring when he headed Vyntra's inviting cross wide a minute before half-time.
Cissé also thought he had given the home side the lead in the 77th minute but he was adjudged to be offside when he headed a free-kick beyond Sergei Ryzhikov.
Nioplias handed 16-year-old midfielder Charis Mavrias his debut in the competition a minute later - the youngster becoming the second-youngest debutant ever in the process behind Celestine Babayaro.
