Ronaldo picked up an injury during the end of the Eurpoean Champions League final, also held in Lison, last week, Xinhua reported.
Portugal were weak in attacking, with both sides seeing poor scoring chances.
The best chance for Portugal came in the first minute, when Eder's header from Nani was saved by Karnezis.
Miguel Veloso's corner in the sixth minute was almost flicked in by Alves but Karnezis managed to tip it over the goalbar.
Veloso's effort from 25 yards in the 26th was also wasted, going well over the cross bar.
Vasilis Torisidis almost scored for Greece in the 38th but his left-footed effort went wide.
Greece were left without Sokratis Papastathopoulos after he was injured when attempting to clear the ball.
After Saturday's poor performance, there are now concerns whether Portugal would be able to make it in the World Cup likely without Ronaldo's presence.