Officials confirmed international military forces carried out the strike against "high-profile" targets in the seaside town of Barawe.
"I can confirm that yesterday, October 4, U.S. military personnel were involved in a counter terrorism operation against a known al-Shabaab terrorist. We are not prepared to provide additional detail at this time," Pentagon Press Secretary George Little said in a statement released Saturday.
Senior U.S. officials say the SEAL team came under fire and had to withdraw before it could confirm whether the target was there, killed or injured.
The U.S. Navy SEAL team was reportedly in a hostile environment following the raid and was forced to withdraw "in order to avoid collateral damage."
No U.S. casualties were reported.
U.S. officials have not confirmed or named who they were after in Somalia, only that the operation was long planned.
The leader of al-Shabab, Mukhtar Abu Zubeyr, also known as Ahmed Godane, claimed responsibility for the terror attack on Nairobi's Westgate Malll in Kenya that left at least 67 people dead last month.
He said it was in retaliation for Kenya's military deployment inside Somalia to prevent a takeover by the militant Islamic Somalia group.
Retired Marine Reserve Lt. Hal Kempfer says more operations in Africa by special forces are likely. North Africa is becoming an area of concern. Saturday's raids could trigger attacks in retaliation.
ABC News and The Associated Press contributed to this report.