The home side had looked on course for a famous victory after opening up a 3-1 lead, but two goals in the final 20 minutes saw Portugal snatch a share of the spoils.
That advantage only lasted 23 minutes after Tomer Hemed reacted fastest to a loose ball to fire the ball into the bottom corner from 12 yards out.
Israel were competing well against their more illustrious opponents and five minutes before half time, they took the lead when Ben Basat beat the offside trap to run through on goal to power the ball past Rui Patricio.
Portugal began the second half on the front foot as they searched for an equaliser, but they were dealt a sucker-punch with 20 minutes to go when Rami Gershon headed home from eight yards.
It appeared as though the hosts were going to hang on, but two minutes into stoppage time, Tal Ben Haim hit the ball against Coentrao, only to see the ball go into the net to earn Portugal a point.