On its Tumblr feed, Anonymous posted a screen grab of the page before it went offline.
The page included pictures of bloodied protesters and a message to the Syrian people predicting that President Bashar al-Assad will fall.
"To the Syrian people: The world stands with you against the brutal regime of Bashar al-Assad," the message said. "Know that time and history are on your side -- tyrants use violence because they have nothing else, and the more violent they are, the more fragile they become.
"All tyrants will fall, and thanks to your bravery, Bashar al-Assad is next," it added.
In a message to the Syrian military, Anonymous said "You are responsible for protecting the Syrian people, and anyone who orders you to kill women, children and the elderly deserves to be tried for treason.
"No outside enemy could do as much damage to Syria as Bashar Al-Assad has done," it said. "Defend your country -- rise up against the regime!"
In apparent retaliation for the hacking, a pro-Syrian government group hacked a site used by Anonymous, posting graphic pictures of what it said were Syrian soldiers killed by protesters.
"In response to your hacking to the website of the Syrian Ministry of Defense, the Syrian people have decided to purify the Internet of your pathetic website," said a message posted at www.anonplus.com.
"Your website has been hacked, and here we leave you these photos showing the scale of terrorism committed by Muslim Brotherhood Organization, whose members have been killing Syrian citizens -- civilians and military."
In a message on Twitter, Helmi Noman, a senior researcher at the University of Toronto's Citizen Lab, said the attack on anonplus.com was carried out by a group calling itself the "Syrian Electronic Army."
Syrian state television reported that Assad had appointed a new defense minister, replacing General Ali Habib with General Daood Rajha, a former army chief.
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