Prime Minister Haider al-Abadi had declared victory on June 17 after IS defences collapsed, with Iraqi forces facing only limited resistance in subsequent clearing operations.
The offensive saw tens of thousands of civilians risk death to flee their homes, leaving Iraq to grapple with a humanitarian crisis as its forces prepare to attack the last remaining major IS hub of Mosul.
"The Iraqi security forces now control the whole city of Fallujah," said Sabah al-Noman, spokesman for the elite counter-terrorism service (CTS) that has been leading the fight.
"Jolan was Daesh's last stronghold in the city and Fallujah is now free of the threat posed by Daesh terrorists," he said, using an Arab acronym for IS.
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"It did not take more than two hours for CTS to retake Jolan. Daesh did not fire a single bullet," Noman said. "This proves that Daesh was defeated even before our forces got there."
A spokesman for the Joint Operations Command coordinating the fight against IS said some jihadist pockets remained northwest of Fallujah and that the overall operation could not be considered over yet.
The offensive began on May 22-23 with an initial phase of staging operations aimed at tightening a months-old siege on Fallujah and led by the Hashed al-Shaabi, a paramilitary organisation dominated by Tehran-backed Shiite militias.
Qassem Suleimani, the powerful head of Iran's elite Revolutionary Guards' overseas operations arm, was more visible than ever before in Iraq during the early days of the operation.
The US-led coalition offered some aerial support but was less involved than six months ago during the operations to retake Ramadi, the capital of Anbar province in which Fallujah is also located.
While some pockets of IS fighters on the outskirts of Fallujah remain to be flushed out, the jihadist organisation does not appear in a position to contest the area any longer.
The loss of Fallujah, which looms large in jihadist mythology and in 2004 saw US forces suffer some of their worst losses since the Vietnam War, is a blow to IS.