"American soldiers, we are coming, watch your back, ISIS," the hackers posted on the US Central Command Twitter feed, using an acronym for the hardline Islamist group, which has taken control of parts of Syria and Iraq.
US officials acknowledged that the incident in which the accounts were "compromised" for about 30 minutes was embarrassing but played down the impact. The FBI said it was investigating.
Pentagon spokesman Army Colonel Steve Warren said the Defence Department "views this as little more than a prank, or as vandalism."
"It's inconvenient, it's an annoyance but in no way is any sensitive or classified information compromised," Warren told a press briefing. Defence officials said in a statement that "operational military networks were not compromised and there was no operational impact."
Islamic State forces have been targeted in air strikes by United States and international partners.
"In the name of Allah, the Most Gracious, the Most Merciful, the CyberCaliphate continues its CyberJihad," the Central Command Twitter feed said after being hacked.
The Twitter account published a list of generals and addresses associated with them, titled "Army General Officer Public Roster (by rank) 2 January 2014."
Subsequent posts read, "Pentagon Networks Hacked! China Scenarios" and "Pentagon Networks Hacked. Korean Scenarios."
Central Command said it was notifying Pentagon and law enforcement authorities about the potential release of "personally identifiable information" and work to make sure the people "potentially affected" are notified quickly.
White House spokesman Josh Earnest said during a press briefing that the hacking was "something that we take seriously." But Earnest added, "There's a pretty significant difference between what is a large data breach and the hacking of a Twitter account."
Even as the hacking was taking place, President Barack Obama on Monday announced new proposals aimed at bolstering American cyber security after high-profile hacking incidents including one against Sony Pictures Entertainment that US officials blamed on North Korea.
Several current and former US security and intelligence officials said until now they had never heard of the CyberCaliphate. Some of the officials expressed skepticism at the groups skills and capabilities.
"Hacking a Twitter is about the equivalent of spray-painting a subway car," a former senior US intelligence official said.
But the chairman of US House of Representatives Committee on Homeland Security, Republican Michael McCaul of Texas, called the incident "severely disturbing."
"Assaults from cyber-jihadists will become more common unless the administration develops a strategy for appropriately responding to these cyberattacks, including those like the North Korea attack against Sony," McCaul said.