The Senate had approved Goss' nomination on a 77-17 vote Wednesday, despite protests from some Democrats who said he would be too political for the position.
At his Senate confirmation hearing Sept. 14, Goss addressed the charges, saying, "I have had times in my life when I have been very nonpartisan. I prefer nonpartisanship. And frankly, what comes more naturally to me is nonpartisanship."
Sen. Jay Rockefeller, W.Va., ranking Democrat on the Senate Intelligence Committee, however, voted against Goss' nomination, saying the congressman repeatedly used intelligence issues for political purposes during his time as chairman of the House Intelligence Committee.
"While I appreciate his testimony and commitment to nonpartisanship if confirmed, I must vote on his record, not his promises," Rockefeller said on the Senate floor.
Senate Intelligence Committee Chairman Pat Roberts, R-Kan., spoke in Goss' favor, saying he is independent, nonpartisan and aggressive -- and qualified for duty outside Congress, the Associated Press reported.
In an Oval Office ceremony Friday, Goss -- accompanied by his family -- was sworn in by White House chief of staff Andy Card with President Bush standing nearby.
Goss succeeds George Tenet, who resigned earlier this summer after serving as director for seven years, during two administrations.
The CIA that Goss now leads faces the possibility of major restructuring in the next few years. A report from the independent commission investigating the Sept. 11 attacks recommended the creation of a national intelligence chief to oversee the CIA and 14 other intelligence agencies.
President Bush and Sen. John Kerry, D-Mass., have both said they support the commission's findings.
If Kerry is elected, he is expected to name a different CIA chief. Neither he nor his running mate Sen. John Edwards, D-N.C., voted on Goss' confirmation.
Goss has represented a southwest Florida district in Congress for 16 years, including eight as House intelligence chairman. He is the second congressman to become CIA director after former President George H.W. Bush.