He shared a meme, since deleted, of a large hand with a Star of David on its wrist, oppressing a group of people.
A caption on it read: "To learn who rules over you, simply find out who you are not allowed to criticise."
The saying, often misattributed to the French philosopher Voltaire, was in fact spoken by white nationalist Kevin Strom.
Cusack added his own comment, "follow the money", to the meme, before later deleting his post after it attracted criticism.
He said he had "mistakenly retweeted an alt-right account" believing the image related to an Israeli hospital bombing.
Apologising for his actions, Cusack said: "It's clear that even if it was Israel's flag & even if you don't have anti-Semitic bone in your body, it is still an anti-Semitic cartoon. Because it deploys anti Jewish stereotypes.
"I [retweeted] and quickly deleted an image that's harmful to both Jewish and Palestinian friends, and for that I'm sorry."
His comments, which he originally blamed on a Twitter bot, drew strong criticism on the social network.
Jewish writer Elad Nehorai asked: "How does a bot 'get you to write 'follow the money' after sharing an overtly anti-Semitic image?"
English comedian David Baddiel, also Jewish, said: "John Cusack says he didn't at first realise that the image was anti-Semitic. My, it's a troublesome old blind spot for progressives, isn't it?"
Anti-Semitism is spiking worldwide, in part fuelled by the rise in online conspiracy theories and fake news.
Reported instances jumped 57% in the US in 2017 compared to the previous year, according to the Anti-Defamation League, with cases reported in every single state for the first time since 2010.
In December, an EU report - based on a survey of 12 European countries - found that anti-Semitism presently pervades European life.