The visitors stunned Israel and silenced the 40,000 capacity crowd with a goal from Bruno Alves in the second minute, but the home side eventually settled down and got back on level terms in the 24th minute through Tomer Hemed.
They then forged a promising lead with goals by Eden Ben Bassat in the 40th minute and Rami Gershon in the 70th.
"The fact that I am so disappointed after a 3-3 draw with Portugal says everything," said Israel coach Eli Guttman.
"We saw a cohesive team that is mentally strong and able to overturn a deficit into a promising lead but we lost concentration after we scored the third goal, as if thinking that the situation was too good to be true and we let [Portugal] back into the game," the downcast coach added.
Portugal coach Paulo Bento said he was generally pleased with his players' performance.
"We started well, although we lost our rhythm and conceded two goals... overall I think we did enough to win the match, we had the majority of goal chances, Israel had three chances and scored three times," he said through an interpreter.
"Having scored a goal in the last minute we could say that we had won a point, but looking at the way we dominated and played, these were two points lost," he added.
Bento thought Portugal's qualifying campaign had been complicated by the draw "but it all depends on us," he said.
