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The final death toll from the attack is now thought to be 695 Israeli civilians, including 36 children, as well as 373 security forces and 71 foreigners, giving a total of 1,139.
It doesn't look like the article you shared is including hostages who have since died. As far as I can tell, there are 59 confirmed dead hostages and Israeli intelligence expects the majority of the unreleased 48 to be dead as well. (Even if only 3 are, that would satisfy the headline.)
Including those (seems pretty weird to not include them) adds up to over 1,200.