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Al-Shabab launched its Twitter account in December 2011, after Kenyan troops went into Somalia to combat it.
Earlier this month, it used Twitter to announce it would kill a French hostage and then said it had done so.
Twitter refused to comment on the suspension but its rules say that threats of violence are banned.
On Wednesday, the al-Shabab account posted a link to a video of two Kenyan civil servants held hostage in Somalia, telling the Kenyan government their lives were in danger unless it released all Muslims held on "so-called terrorism charges" in the country, reports Reuters news agency.
Al-Shabab, which is affiliated to al-Qaeda, said it killed French intelligence agent Denis Allex in retaliation for a failed French operation to free him.
The French government has said it believes Mr Allex was killed during the raid two weeks ago, in which two French commandos also died.
Mr Allex - a French spy - was kidnapped in Somalia in July 2009.
Al-Shabab has been forced out of Somali