"I can confirm that Captain Phillips has been safely recovered," she said.
Three of the four pirates holding Phillips were killed in the operation while the fourth was taken into custody, US officials said.
Al Jazeera's correspondent Mohammed Adow said: "US forces are reported to have attacked the lifeboat when the pirates were expecting a diplomatic exchange ... [and] have taken the remaining pirate to one of their ships in these waters."
"The ransom money pirates have been getting is so huge, that many more people have been drawn into the activity.
"It is something that has become a very lucrative trend."
Captain 'a hero'
Barack Obama, the US president, had given authority to use force against the pirates, and a commander acted when he concluded the pirates were about to kill the hostage with machine guns, a US Navy official said.
"They were pointing the AK-47s at the captain," Vice Admiral William Gortney, head of the US Naval Central Command, said in a Pentagon briefing from Bahrain.
"The United States government policy is to not negotiate," he said.
Phillips was taken aboard the USS Bainbridge, one of the two US naval warships involved in the standoff with the pirates, after his safe release, the American news network CNN reported.
The pirates had kept hold of Phillips on board a lifeboat after releasing the Maersk Alabama and its crew. He reportedly jumped from the vessel on Friday in an attempt to escape, but was quickly re-captured.
Relatives said Phillips had volunteered to join the pirates in their lifeboat in exchange for the safety of his crew. The pirates demanded a $2m ransom in exchange for him.
The crew of the Maersk Alabama hailed Phillips a hero after they arrived in Mombasa on board the 17,000-tonne vessel, with one crew member saying: "He saved our lives by giving himself up."
Obama pledge
Barack Obama, the US president, gave permission to use his country's military to rescue Phillips, US officials said.
Obama welcomed Phillip's release and said the US remained resolved to halt the rise of piracy off the Somali coast.
"To achieve that goal, we must continue to work with our partners to prevent future attacks, be prepared to interdict acts of piracy and ensure that those who commit acts of piracy are held accountable for their crimes."
Tens of millions of dollars in ransoms are believed to have been paid for the release of vessels captured in recent months.
'Major event'
Ali Abdullahi, a security consultant and risk management analyst specialising on Somalia, said the only way to tackle piracy was to address the political and economic problems there.
"A lot of the time, we're not talking about the core issues which have made piracy a major event in Somalia," he told Al Jazeera.
"There has been a lot of illegal fishing by international agents, toxic waste dumping on parts of Somalia, a lack of bad governance as well, all of which are the real causes of piracy."
Hijackings are an ongoing problem in the busy shipping lanes off the coast of Somalia.
At least a dozen ships have been seized in the Indian Ocean and more than 200 crew members are being held hostage.