The threat was lifted on Saturday afternoon
The federation posted an update at 3.30pm on Saturday to say they had been told there was no “known imminent threat” and that services could safely resume.
The initial threat, posted just before midday, said that security staff at synagogues and community centres had been placed on the “highest alert”.
“In an abundance of caution, we are taking all appropriate steps to ensure the safety of the community,” the organisation said in a Facebook post.
“After communicating with all local synagogues and organisations, it was recommended that all formal Jewish gatherings be suspended until further notice.”
The federation asked that any suspicious activity be reported to law enforcement.
In a statement on Saturday afternoon, the FBI said it was investigating a potential threat at an “unidentified synagogue in Texas”.
“We are working to determine the credibility of the threat and sharing information with our law enforcement partners and our partners in the Jewish community,” the FBI said.
The San Antonio Police Department said it was in communication with the FBI.
In April, the Anti Defamation League warned anti-semitic attacks were increasing in the San Antonio area.