A goal from Ricardo Costa just before the half-hour put the Iberians in front but they were unable to increase their advantage as they failed to convert their early dominance into chances.
Indeed, Israel almost took the lead against the run of play when Cristiano Ronaldo was dispossessed by Tal Ben-Haim who strode forward and set up Maharan Radi, but he dragged his effort wide from the edge of the area.
The visitors started the second half far brighter than they did the first but it was the Portuguese who nearly found a way through when Ronaldo's trickery and cross found Hugo Almeida who somehow headed over when it was easier to score.
He nearly did nab a goal on 52 minutes when he nodded home only to find he'd strayed offside.
As the game progressed, the hosts still squandered attacking positions and were made to pay as keeper Rui Patricio inexplicably gave the ball to Ben Basat, who slotted it home with five minutes remaining.
Israel held on to draw and it means that Portugal will almost certainly be in the playoffs, with Russia three points ahead and with a significantly weaker goal difference.
Russia travel to Azerbaijan on Tuesday knowing that a draw means they qualify automatically for the finals no matter what Portugal can do at home to Luxembourg.