The West Ham United midfielder was one of a number surprise omissions from a list of 23 named ahead of the October 12 clash in Luxembourg and the return fixture in Tel Aviv four days later.
Guttman offered no explanation for the move in statement issued by the Israel Football Association, but local media reports said players had been dropped because they were not getting regular playing time at their clubs.
Israel's campaign got off to a poor start last month with a 1-1 away draw against Azerbaijan followed by a 4-0 home drubbing by Russia, their worst start in qualifying since 1994.
Benayoun, 32, had made 90 international appearances for Israel, second on the all-time list, and scored 24 goals. He had been Israel's regular captain since 2008.
Strikers Itai Shechter of Swansea City and Hertha Berlin's Ben Sahar, and Nuremburg midfielder Almog Cohen were also omitted.
