John William Racine II, 24, replaced the controversial Arab satellite TV with a logo featuring the American flag and the message "Let Freedom Ring".
The attack also came with a message that told visitors that the site had been "hacked by Patriot, Freedom Cyber Force Militia".
The attack came after Al Jazeera showed images of dead and captured British and American soldiers during the war, provided to it by the Iraqi regime, which were condemned by Tony Blair and George Bush.
The station has faced charges that it was infiltrated by agents of Iraq's secret intelligence service, and its managing director has since resigned.
Racine hacked both the Al Jazeera Arabic and English-language websites, which were attacked several times during the fighting in Iraq.
Visitors to the English-language site saw the flag shaped like a map of America, while those who went to the Arabic site were redirected to a pornography site.
It is understood that Racine turned himself into authorities shortly after he attacked the Al Jazeera website. He has agreed to plead guilty to two charges of wire fraud and unlawful interception of an electronic communication and is due to appear in court in Los Angeles on Monday.
According to a report on the BBC, it is expected that he will be sentenced to three years' probation, 1,000 hours of community service and a fine of $1,500.
The decision was welcomed by Al Jazeera, but said it was unlikely that the attack was carried out by just one person.
Al Jazeera spokesman Salah Siddiki said: "It is not difficult for one person to have the brain to do this, but the financial capabilities needed for the hacking are hard to find with one person."
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